Serialized Form (Gemma 1.32.2-SNAPSHOT Test API)

Package ubic.gemma.core.analysis.expression.coexpression.links
- Class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - absoluteValue
      
      boolean absoluteValue
    - arrayName
      
      String arrayName
    - cdfCut
      
      double cdfCut
    - checkCorrelationDistribution
      
      boolean checkCorrelationDistribution
    - checkForBatchEffect
      
      boolean checkForBatchEffect
    - checkForOutliers
      
      boolean checkForOutliers
    - correlationCacheThreshold
      
      double correlationCacheThreshold
    - fwe
      
      double fwe
    - lowerCdfCutUsed
      
      boolean lowerCdfCutUsed
    - lowerTailCut
      
      double lowerTailCut
    - makeSampleCorrMatImages
      
      boolean makeSampleCorrMatImages
    - metric
      
      String metric
    - minNumPresent
      
      int minNumPresent
    - normalizationMethod
      
      ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod normalizationMethod
    - omitNegLinks
      
      boolean omitNegLinks
    - outputFile
      
      File outputFile
    - probeDegreeThreshold
      
      int probeDegreeThreshold
    - singularThreshold
      
      ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold singularThreshold
    - subset
      
      boolean subset
    - subsetSize
      
      double subsetSize
    - subsetUsed
      
      boolean subsetUsed
    - textOut
      
      boolean textOut
    - upperCdfCutUsed
      
      boolean upperCdfCutUsed
    - upperTailCut
      
      double upperTailCut
    - useDb
      
      boolean useDb
- Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -4436136164850796179L
Package ubic.gemma.core.analysis.expression.diff
- Class ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException extends ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.AnalysisException extends RuntimeException implements Serializable
  - Serialized Fields
    - config
      
      ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig config
- Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable
  - Serialized Fields
    - activeExperiments
      
      Collection<ubic.gemma.model.expression.experiment.BioAssaySet> activeExperiments
    - fisherPValue
      
      Double fisherPValue
    - gene
      
      ubic.gemma.model.genome.gene.GeneValueObject gene
    - numExperimentsInScope
      
      int numExperimentsInScope
    - numMetThreshold
      
      int numMetThreshold
    - numSearchedExperiments
      
      int numSearchedExperiments
    - probeResults
      
      Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject> probeResults
    - sortKey
      
      String sortKey
- Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - eeId
      
      Long eeId
    - efId
      
      Long efId
- Class ubic.gemma.core.analysis.expression.diff.EbayesFailureException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable
- Class ubic.gemma.core.analysis.expression.diff.NoSampleLeftForAnalysisException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable
Package ubic.gemma.core.analysis.preprocess
- Class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      ubic.gemma.core.analysis.preprocess.filter.FilteringException cause
- Class ubic.gemma.core.analysis.preprocess.InsufficientProbesException extends ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ubic.gemma.core.analysis.preprocess.PreprocessingException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -8463478950898408838L
- Class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException cause
- Class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException cause
- Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable
  - Serialized Fields
    - cause
      
      ubic.gemma.core.analysis.preprocess.svd.SVDException cause
Package ubic.gemma.core.analysis.preprocess.batcheffects
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound extends Object implements Serializable
  - Serialized Fields
    - chiSquare
      
      double chiSquare
    - df
      
      int df
    - ee
      
      ubic.gemma.model.expression.experiment.BioAssaySet ee
    - ef
      
      ubic.gemma.model.expression.experiment.ExperimentalFactor ef
    - numBatches
      
      int numBatches
    - p
      
      double p
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException extends ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException implements Serializable
- Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable
  
  serialVersionUID:
  
  -1770591991479420212L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException extends ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1917074433646650950L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException extends ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  9088141067684148902L
- Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException extends ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException implements Serializable
  
  serialVersionUID:
  
  1L
Package ubic.gemma.core.analysis.preprocess.convert
- Class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException extends Exception implements Serializable
- Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException extends ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException implements Serializable
Package ubic.gemma.core.analysis.preprocess.detect
- Class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException extends ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException implements Serializable
  - Serialized Fields
    - inferredQuantitationType
      
      ubic.gemma.model.common.quantitationtype.QuantitationType inferredQuantitationType
- Class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException extends ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException implements Serializable
  - Serialized Fields
    - quantitationType
      
      ubic.gemma.model.common.quantitationtype.QuantitationType quantitationType
- Class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException extends Exception implements Serializable
- Class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException extends ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException implements Serializable
  - Serialized Fields
    - suspiciousValues
      
      List<ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult> suspiciousValues

Package ubic.gemma.core.analysis.preprocess.svd

Class ubic.gemma.core.analysis.preprocess.svd.SVDException extends Exception implements Serializable

Class ubic.gemma.core.analysis.preprocess.svd.SVDResult extends Object implements Serializable

Serialized Fields

bioAssays

List<ubic.gemma.model.expression.bioAssay.BioAssay> bioAssays

bioMaterials

List<ubic.gemma.model.expression.biomaterial.BioMaterial> bioMaterials

dateCorrelations
```
Map<Integer,Double> dateCorrelations
```
datePVals
```
Map<Integer,Double> datePVals
```
dates
```
List<Date> dates
```

experimentAnalyzed

ubic.gemma.model.expression.experiment.BioAssaySet experimentAnalyzed

factorCorrelations

Map<Integer,Map<ubic.gemma.model.expression.experiment.ExperimentalFactor,Double>> factorCorrelations

factorPVals

Map<Integer,Map<ubic.gemma.model.expression.experiment.ExperimentalFactor,Double>> factorPVals

factors

Map<ubic.gemma.model.expression.experiment.ExperimentalFactor,List<Number>> factors

variances
```
double[] variances
```

vMatrix

DoubleMatrix<ubic.gemma.model.expression.biomaterial.BioMaterial,Integer> vMatrix

Package ubic.gemma.core.analysis.report
- Class ubic.gemma.core.analysis.report.AuditableObject extends Object implements Serializable
  
  serialVersionUID:
  
  -7862129089784691035L
  - Serialized Fields
    - date
      
      Date date
    - id
      
      Long id
    - type
      
      String type

Package ubic.gemma.core.analysis.sequence

Class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject extends Object implements Serializable

Serialized Fields

arrayDesignId
```
Long arrayDesignId
```
arrayDesignName
```
String arrayDesignName
```
arrayDesignShortName
```
String arrayDesignShortName
```
bioSequenceId
```
String bioSequenceId
```
bioSequenceName
```
String bioSequenceName
```
bioSequenceNcbiId
```
String bioSequenceNcbiId
```
compositeSequenceDescription
```
String compositeSequenceDescription
```
compositeSequenceId
```
String compositeSequenceId
```
compositeSequenceName
```
String compositeSequenceName
```

geneProducts

Map<Long,ubic.gemma.model.genome.gene.GeneProductValueObject> geneProducts

genes

Map<Long,ubic.gemma.model.genome.gene.GeneValueObject> genes

numBlatHits
```
Integer numBlatHits
```

Class ubic.gemma.core.analysis.sequence.GeneMappingSummary extends Object implements Serializable

serialVersionUID:: 8899320580201273360L

Serialized Fields

blatResult

ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject blatResult

blatResultId
```
String blatResultId
```

compositeSequence

ubic.gemma.model.expression.designElement.CompositeSequenceValueObject compositeSequence

geneProductIdGeneMap

Map<String,ubic.gemma.model.genome.gene.GeneValueObject> geneProductIdGeneMap

geneProductIdMap

Map<String,ubic.gemma.model.genome.gene.GeneProductValueObject> geneProductIdMap

geneProductMap

Map<ubic.gemma.model.genome.gene.GeneProductValueObject,ubic.gemma.model.genome.gene.GeneValueObject> geneProductMap

identity
```
double identity
```
score
```
double score
```

Package ubic.gemma.core.analysis.singleCell.aggregate
- Class ubic.gemma.core.analysis.singleCell.aggregate.AggregationException extends RuntimeException implements Serializable
- Class ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForAggregationException extends ubic.gemma.core.analysis.singleCell.aggregate.AggregationException implements Serializable
Package ubic.gemma.core.job
- Class ubic.gemma.core.job.TaskCommand extends Object implements Serializable
  - Serialized Fields
    - emailAlert
      
      boolean emailAlert
    - maxQueueMillis
      
      long maxQueueMillis
    - maxRuntimeMillis
      
      long maxRuntimeMillis
    - persistJobDetails
      
      Boolean persistJobDetails
    - securityContext
      
      org.springframework.security.core.context.SecurityContext securityContext
    - submitter
      
      String submitter
- Class ubic.gemma.core.job.TaskResult extends Object implements Serializable
  - Serialized Fields
    - answer
      
      Serializable answer
Package ubic.gemma.core.job.progress
- Class ubic.gemma.core.job.progress.ProgressData extends Object implements Serializable
  
  serialVersionUID:
  
  -4303625064082352461L
  - Serialized Fields
    - description
      
      String description
    - done
      
      boolean done
    - failed
      
      boolean failed
    - forwardingURL
      
      String forwardingURL
    - percent
      
      int percent
    - taskId
      
      String taskId
Package ubic.gemma.core.loader.entrez
- Class ubic.gemma.core.loader.entrez.EntrezException extends RuntimeException implements Serializable
  - Serialized Fields
    - errors
      
      List<String> errors
Package ubic.gemma.core.loader.expression.arrayDesign
- Class ubic.gemma.core.loader.expression.arrayDesign.Reporter extends ubic.gemma.model.common.AbstractDescribable implements Serializable
  
  serialVersionUID:
  
  3703827938981026012L
  - Serialized Fields
    - col
      
      Integer col
    - compositeSequence
      
      ubic.gemma.model.expression.designElement.CompositeSequence compositeSequence
    - immobilizedCharacteristic
      
      ubic.gemma.model.genome.biosequence.BioSequence immobilizedCharacteristic
    - row
      
      Integer row
    - startInBioChar
      
      Long startInBioChar
    - strand
      
      String strand
Package ubic.gemma.core.loader.expression.geo
- Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence extends Object implements Serializable
  
  serialVersionUID:
  
  -5285504953530483114L
  - Serialized Fields
    - accToDataset
      
      Map<String,String> accToDataset
    - accToTitle
      
      Map<String,String> accToTitle
    - sets
      
      Collection<Set<String>> sets
Package ubic.gemma.core.loader.util
- Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  5677999264920938691L
  - Serialized Fields
    - data
      
      Object data
Package ubic.gemma.core.loader.util.anndata
- Class ubic.gemma.core.loader.util.anndata.AnnDataException extends RuntimeException implements Serializable
- Class ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException extends ubic.gemma.core.loader.util.anndata.AnnDataException implements Serializable
- Class ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException extends ubic.gemma.core.loader.util.anndata.AnnDataException implements Serializable
Package ubic.gemma.core.loader.util.biomart
- Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -859220901359582113L
  - Serialized Fields
    - enemblTranscriptId
      
      String enemblTranscriptId
    - ensembleGeneId
      
      String ensembleGeneId
    - ensemblPeptideId
      
      String ensemblPeptideId
    - hgcnId
      
      String hgcnId
    - ncbiGenes
      
      Collection<String> ncbiGenes
    - ncbiTaxonId
      
      Integer ncbiTaxonId
Package ubic.gemma.core.loader.util.hdf5
- Class ubic.gemma.core.loader.util.hdf5.H5Exception extends RuntimeException implements Serializable
  - Serialized Fields
    - cause
      
      hdf.hdf5lib.exceptions.HDF5Exception cause
- Class ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException extends IOException implements Serializable
Package ubic.gemma.core.ontology
- Class ubic.gemma.core.ontology.AbstractOntologyResourceSimple extends Object implements Serializable
  - Serialized Fields
    - label
      
      String label
    - uri
      
      String uri
- Class ubic.gemma.core.ontology.OntologyIndividualSimple extends ubic.gemma.core.ontology.AbstractOntologyResourceSimple implements Serializable
  - Serialized Fields
    - instanceOf
      
      OntologyTermSimple instanceOf
- Class ubic.gemma.core.ontology.OntologyPropertySimple extends ubic.gemma.core.ontology.AbstractOntologyResourceSimple implements Serializable
Package ubic.gemma.core.search
- Class ubic.gemma.core.search.BaseCodeOntologySearchException extends ubic.gemma.core.search.SearchException implements Serializable
  - Serialized Fields
    - cause
      
      OntologySearchException cause
- Class ubic.gemma.core.search.ParseSearchException extends ubic.gemma.core.search.SearchException implements Serializable
  - Serialized Fields
    - originalParseException
      
      ubic.gemma.core.search.ParseSearchException originalParseException
    - query
      
      String query
- Class ubic.gemma.core.search.SearchException extends Exception implements Serializable
- Class ubic.gemma.core.search.SearchTimeoutException extends ubic.gemma.core.search.SearchException implements Serializable
  - Serialized Fields
    - cause
      
      TimeoutException cause
Package ubic.gemma.core.search.lucene
- Class ubic.gemma.core.search.lucene.LuceneParseSearchException extends ubic.gemma.core.search.ParseSearchException implements Serializable
Package ubic.gemma.core.search.source
- Class ubic.gemma.core.search.source.HibernateSearchException extends ubic.gemma.core.search.SearchException implements Serializable
  - Serialized Fields
    - cause
      
      org.hibernate.search.SearchException cause
Package ubic.gemma.core.util
- Class ubic.gemma.core.util.GemmaRestApiClientException extends RuntimeException implements Serializable
- Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo extends Object implements Serializable
- Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestImplicitValueObject extends Object implements Serializable

Package ubic.gemma.core.visualization

Class ubic.gemma.core.visualization.ExpressionDataHeatmap extends Object implements Serializable

Serialized Fields

bioAssaySet

ubic.gemma.model.expression.experiment.BioAssaySet bioAssaySet

cellLevelCharacteristics

ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics cellLevelCharacteristics

cellSize
```
int cellSize
```

designElements

ubic.gemma.persistence.util.Slice<ubic.gemma.model.expression.designElement.CompositeSequence> designElements

dimension

ubic.gemma.model.expression.bioAssayData.BioAssayDimension dimension

focusedCellLevelCharacteristic

ubic.gemma.model.common.description.Characteristic focusedCellLevelCharacteristic

genes

List<ubic.gemma.model.genome.Gene> genes

sampleIndex
```
int[] sampleIndex
```

samples

List<ubic.gemma.model.expression.bioAssay.BioAssay> samples

singleCellQuantitationType

ubic.gemma.model.common.quantitationtype.QuantitationType singleCellQuantitationType

transpose
```
boolean transpose
```

vectors

ubic.gemma.persistence.util.Slice<? extends ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector> vectors

Class ubic.gemma.core.visualization.SingleCellSparsityHeatmap extends Object implements Serializable

Serialized Fields

cellSize
```
int cellSize
```

designElementsPerSample

Map<ubic.gemma.model.expression.bioAssay.BioAssay,Long> designElementsPerSample

dimension

ubic.gemma.model.expression.bioAssayData.BioAssayDimension dimension

expressionExperiment

ubic.gemma.model.expression.experiment.ExpressionExperiment expressionExperiment

samples

List<ubic.gemma.model.expression.bioAssay.BioAssay> samples

singleCellDimension

ubic.gemma.model.expression.bioAssayData.SingleCellDimension singleCellDimension

subSets

List<ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet> subSets

transpose
```
boolean transpose
```

type

ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType type

Package ubic.gemma.model.analysis.expression.diff
- Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.analysis.expression.diff.ContrastResult> implements Serializable
  - Serialized Fields
    - coefficient
      
      Double coefficient
    - factorValue
      
      ubic.gemma.model.expression.experiment.FactorValueBasicValueObject factorValue
    - factorValueId
      
      Long factorValueId
    - logFoldChange
      
      Double logFoldChange
    - pvalue
      
      Double pvalue
    - secondFactorValue
      
      ubic.gemma.model.expression.experiment.FactorValueBasicValueObject secondFactorValue
    - secondFactorValueId
      
      Long secondFactorValueId
    - tStat
      
      Double tStat
- Class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
      
      List<ubic.gemma.model.analysis.expression.diff.ContrastVO> contrasts
    - resultId
      
      Long resultId
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject extends ubic.gemma.model.analysis.AnalysisResultSetValueObject<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult,ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet> implements Serializable
  - Serialized Fields
    - analysis
      
      ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject analysis
    - baselineGroup
      
      ubic.gemma.model.expression.experiment.FactorValueBasicValueObject baselineGroup
    - experimentalFactors
      
      Collection<ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject> experimentalFactors
    - results
      
      Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject> results
    - secondBaselineGroup
      
      ubic.gemma.model.expression.experiment.FactorValueBasicValueObject secondBaselineGroup
    - taxa
      
      Set<ubic.gemma.model.genome.TaxonValueObject> taxa
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject extends ubic.gemma.model.analysis.AnalysisResultValueObject<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult> implements Serializable
  - Serialized Fields
    - contrasts
      
      List<ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject> contrasts
    - correctedPvalue
      
      Double correctedPvalue
    - genes
      
      List<ubic.gemma.model.genome.gene.GeneValueObject> genes
    - probeId
      
      Long probeId
    - probeName
      
      String probeName
    - pValue
      
      Double pValue
    - rank
      
      Double rank
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject extends ubic.gemma.model.analysis.AnalysisValueObject<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis> implements Serializable
  
  serialVersionUID:
  
  622877438067070041L
  - Serialized Fields
    - arrayDesignsUsed
      
      Collection<Long> arrayDesignsUsed
    - experimentAnalyzedId
      
      Long experimentAnalyzedId
    - factorValuesUsed
      
      Map<Long,Collection<ubic.gemma.model.expression.experiment.FactorValueValueObject>> factorValuesUsed
    - resultSets
      
      Collection<ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject> resultSets
    - sourceExperimentId
      
      Long sourceExperimentId
    - subsetFactor
      
      ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject subsetFactor
    - subsetFactorId
      
      Long subsetFactorId
    - subsetFactorValue
      
      ubic.gemma.model.expression.experiment.FactorValueValueObject subsetFactorValue
    - subsetFactorValueId
      
      Long subsetFactorValueId
- Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject extends Object implements Serializable
  - Serialized Fields
    - contrasts
      
      ubic.gemma.model.analysis.expression.diff.ContrastsValueObject contrasts
    - corrP
      
      Double corrP
    - direction
      
      ubic.gemma.model.analysis.expression.diff.Direction direction
    - experimentalFactors
      
      Collection<ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject> experimentalFactors
    - expressionExperiment
      
      ubic.gemma.model.expression.experiment.BioAssaySetValueObject expressionExperiment
    - fisherContribution
      
      Boolean fisherContribution
    - gene
      
      ubic.gemma.model.genome.gene.GeneValueObject gene
    - id
      
      Long id
    - metThreshold
      
      Boolean metThreshold
    - p
      
      Double p
    - probe
      
      String probe
    - probeId
      
      Long probeId
    - resultSetId
      
      Long resultSetId
    - sortKey
      
      String sortKey
- Class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult extends Object implements Serializable
  
  serialVersionUID:
  
  -6199218806972657112L
  - Serialized Fields
    - analysisResultId
      
      Long analysisResultId
    - correctedPvalue
      
      Double correctedPvalue
    - geneId
      
      Long geneId
    - numberOfProbes
      
      int numberOfProbes
    - numberOfProbesDiffExpressed
      
      int numberOfProbesDiffExpressed
    - pvalue
      
      Double pvalue
    - resultSetId
      
      Long resultSetId
    - score
      
      Double score
- Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  2063274043081170625L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - arrayDesignsUsed
      
      Collection<Long> arrayDesignsUsed
    - baselineGroup
      
      ubic.gemma.model.expression.experiment.FactorValueValueObject baselineGroup
    - bioAssaySetAnalyzedId
      
      Long bioAssaySetAnalyzedId
    - downregulatedCount
      
      Integer downregulatedCount
    - experimentalFactors
      
      Collection<ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject> experimentalFactors
    - factorIds
      
      Collection<Long> factorIds
    - id
      
      Long id
    - numberOfDiffExpressedProbes
      
      Integer numberOfDiffExpressedProbes
    - numberOfGenesAnalyzed
      
      Integer numberOfGenesAnalyzed
    - numberOfProbesAnalyzed
      
      Integer numberOfProbesAnalyzed
    - qValue
      
      Double qValue
    - threshold
      
      Double threshold
    - upregulatedCount
      
      Integer upregulatedCount
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  3868004995989355452L
  - Serialized Fields
    - includedResultSetsInfo
      
      Collection<ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject> includedResultSetsInfo
    - numGenesAnalyzed
      
      Integer numGenesAnalyzed
    - results
      
      Collection<ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject> results
- Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6099286095885830140L
  - Serialized Fields
    - geneName
      
      String geneName
    - geneSymbol
      
      String geneSymbol
    - metaPvalue
      
      Double metaPvalue
    - metaQvalue
      
      Double metaQvalue
    - upperTail
      
      Boolean upperTail
- Class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  -4660741839991839187L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentId
      
      Long experimentId
    - resultSetId
      
      Long resultSetId
Package ubic.gemma.model.association.coexpression
- Class ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject extends Object implements Serializable
  - Serialized Fields
    - geneId
      
      Long geneId
    - nodeDegreesNeg
      
      TreeMap<Integer,Integer> nodeDegreesNeg
    - nodeDegreesPos
      
      TreeMap<Integer,Integer> nodeDegreesPos
    - relDegreesNeg
      
      TreeMap<Integer,Double> relDegreesNeg
    - relDegreesPos
      
      TreeMap<Integer,Double> relDegreesPos
Package ubic.gemma.model.common.description
- Class ubic.gemma.model.common.description.AnnotationValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.common.description.Characteristic> implements Serializable
  - Serialized Fields
    - className
      
      String className
    - classUri
      
      String classUri
    - description
      
      String description
    - evidenceCode
      
      String evidenceCode
    - objectClass
      
      String objectClass
    - parentDescription
      
      String parentDescription
    - parentLink
      
      String parentLink
    - parentName
      
      String parentName
    - parentOfParentDescription
      
      String parentOfParentDescription
    - parentOfParentLink
      
      String parentOfParentLink
    - parentOfParentName
      
      String parentOfParentName
    - termName
      
      String termName
    - termUri
      
      String termUri
- Class ubic.gemma.model.common.description.BibliographicReferenceValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.common.description.BibliographicReference> implements Serializable
  - Serialized Fields
    - abstractText
      
      String abstractText
    - authorList
      
      String authorList
    - chemicalsTerms
      
      Collection<String> chemicalsTerms
    - citation
      
      ubic.gemma.model.common.description.CitationValueObject citation
    - experiments
      
      Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> experiments
    - issue
      
      String issue
    - meshTerms
      
      Collection<String> meshTerms
    - pages
      
      String pages
    - pubAccession
      
      String pubAccession
    - publication
      
      String publication
    - publicationDate
      
      Date publicationDate
    - publisher
      
      String publisher
    - retracted
      
      boolean retracted
    - title
      
      String title
    - volume
      
      String volume
- Class ubic.gemma.model.common.description.CharacteristicValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.common.description.Characteristic> implements Serializable
  - Serialized Fields
    - alreadyPresentInDatabase
      
      boolean alreadyPresentInDatabase
    - alreadyPresentOnGene
      
      boolean alreadyPresentOnGene
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - child
      
      boolean child
    - numTimesUsed
      
      int numTimesUsed
    - ontologyUsed
      
      String ontologyUsed
    - originalValue
      
      String originalValue
    - privateGeneCount
      
      long privateGeneCount
    - publicGeneCount
      
      long publicGeneCount
    - root
      
      boolean root
    - taxon
      
      String taxon
    - urlId
      
      String urlId
    - value
      
      String value
    - valueDefinition
      
      String valueDefinition
    - valueId
      
      String valueId
    - valueUri
      
      String valueUri
- Class ubic.gemma.model.common.description.CitationValueObject extends Object implements Serializable
  - Serialized Fields
    - citation
      
      String citation
    - id
      
      Long id
    - pubmedAccession
      
      String pubmedAccession
    - pubmedURL
      
      String pubmedURL
    - retracted
      
      boolean retracted
- Class ubic.gemma.model.common.description.DatabaseEntryValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.common.description.DatabaseEntry> implements Serializable
  
  serialVersionUID:
  
  -527323410580090L
  - Serialized Fields
    - accession
      
      String accession
    - externalDatabase
      
      ubic.gemma.model.common.description.ExternalDatabaseValueObject externalDatabase
- Class ubic.gemma.model.common.description.ExternalDatabaseValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.common.description.ExternalDatabase> implements Serializable
  
  serialVersionUID:
  
  -1714429166594162374L
  - Serialized Fields
    - checked
      
      boolean checked
    - description
      
      String description
    - externalDatabases
      
      Set<ubic.gemma.model.common.description.ExternalDatabaseValueObject> externalDatabases
    - lastUpdated
      
      Date lastUpdated
    - name
      
      String name
    - releaseUrl
      
      URL releaseUrl
    - releaseVersion
      
      String releaseVersion
    - uri
      
      String uri

Package ubic.gemma.model.common.search

Class ubic.gemma.model.common.search.SearchSettingsValueObject extends Object implements Serializable

serialVersionUID:: -934534534L

Serialized Fields

maxResults
```
Integer maxResults
```

platformConstraint

ubic.gemma.model.expression.arrayDesign.ArrayDesign platformConstraint

query
```
String query
```
searchBibrefs
```
Boolean searchBibrefs
```
searchBioSequences
```
Boolean searchBioSequences
```
searchExperiments
```
Boolean searchExperiments
```
searchExperimentSets
```
Boolean searchExperimentSets
```
searchGenes
```
Boolean searchGenes
```
searchGeneSets
```
Boolean searchGeneSets
```
searchPlatforms
```
Boolean searchPlatforms
```
searchProbes
```
Boolean searchProbes
```
taxon
```
ubic.gemma.model.genome.Taxon taxon
```
termUri
```
String termUri
```
useCharacteristics
```
Boolean useCharacteristics
```
useDatabase
```
Boolean useDatabase
```
useGo
```
Boolean useGo
```
useIndices
```
Boolean useIndices
```

Package ubic.gemma.model.expression.bioAssayData
- Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.bioAssayData.BioAssayDimension> implements Serializable
  
  serialVersionUID:
  
  -8686807689616396835L
  - Serialized Fields
    - bioAssays
      
      List<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> bioAssays
    - description
      
      String description
      
      Deprecated.
    - isReordered
      
      boolean isReordered
    - isSubset
      
      boolean isSubset
    - name
      
      String name
      
      Deprecated.
    - sourceBioAssayDimension
      
      ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject sourceBioAssayDimension
- Class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject extends ubic.gemma.model.expression.bioAssayData.DataVectorValueObject implements Serializable
  - Serialized Fields
    - data
      
      boolean[] data
- Class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics> implements Serializable
  - Serialized Fields
    - characteristicIds
      
      List<Long> characteristicIds
    - characteristics
      
      Set<ubic.gemma.model.common.description.CharacteristicValueObject> characteristics
    - numberOfAssignedCells
      
      Integer numberOfAssignedCells
- Class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.bioAssayData.DataVector> implements Serializable
  - Serialized Fields
    - bioAssayDimension
      
      ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject bioAssayDimension
    - designElement
      
      ubic.gemma.model.expression.designElement.CompositeSequenceValueObject designElement
    - expressionExperiment
      
      ubic.gemma.model.expression.experiment.BioAssaySetValueObject expressionExperiment
    - genes
      
      Collection<Long> genes
    - quantitationType
      
      ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject quantitationType
- Class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject extends ubic.gemma.model.expression.bioAssayData.DataVectorValueObject implements Serializable
  - Serialized Fields
    - data
      
      double[] data
    - masked
      
      boolean masked
    - pvalue
      
      Double pvalue
    - rank
      
      Double rank
    - rankByMax
      
      Double rankByMax
    - rankByMean
      
      Double rankByMean
    - reorganized
      
      boolean reorganized
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject extends Object implements Serializable
  - Serialized Fields
    - datasetId
      
      long datasetId
    - geneExpressionLevels
      
      LinkedList<ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> geneExpressionLevels
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject extends Object implements Serializable
  - Serialized Fields
    - elements
      
      List<ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject> elements
    - geneNcbiId
      
      Integer geneNcbiId
    - geneOfficialSymbol
      
      String geneOfficialSymbol
- Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject extends Object implements Serializable
  - Serialized Fields
    - bioAssayExpressionLevels
      
      Map<String,Double> bioAssayExpressionLevels
    - designElementName
      
      String designElementName
- Class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.bioAssayData.SingleCellDimension> implements Serializable
  - Serialized Fields
    - bioAssayIds
      
      List<Long> bioAssayIds
    - cellIds
      
      List<String> cellIds
    - cellLevelCharacteristics
      
      Set<ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject> cellLevelCharacteristics
    - cellTypeAssignments
      
      Set<ubic.gemma.model.analysis.CellTypeAssignmentValueObject> cellTypeAssignments
    - numberOfCells
      
      int numberOfCells
- Class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject extends ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject implements Serializable
  - Serialized Fields
    - sourceVectorId
      
      Long sourceVectorId
Package ubic.gemma.model.expression.experiment
- Class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.experiment.FactorValue> implements Serializable
  - Serialized Fields
    - characteristics
      
      List<ubic.gemma.model.common.description.CharacteristicValueObject> characteristics
    - experimentalFactorCategory
      
      ubic.gemma.model.common.description.CharacteristicValueObject experimentalFactorCategory
    - experimentalFactorId
      
      Long experimentalFactorId
    - experimentalFactorType
      
      String experimentalFactorType
    - measurementObject
      
      ubic.gemma.model.common.measurement.MeasurementValueObject measurementObject
    - ontologyId
      
      String ontologyId
    - statements
      
      List<ubic.gemma.model.expression.experiment.StatementValueObject> statements
    - summary
      
      String summary
- Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.experiment.ExperimentalFactor> implements Serializable
  
  serialVersionUID:
  
  -2615804031123874251L
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - description
      
      String description
    - factorValues
      
      String factorValues
      
      Deprecated.
    - name
      
      String name
    - type
      
      String type
    - values
      
      Collection<ubic.gemma.model.expression.experiment.FactorValueValueObject> values
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject implements Serializable
  
  serialVersionUID:
  
  -1219449523930648392L
  - Serialized Fields
    - arrayDesigns
      
      Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> arrayDesigns
    - batchFetchEventType
      
      String batchFetchEventType
    - dateArrayDesignLastUpdated
      
      Date dateArrayDesignLastUpdated
    - dateBatchFetch
      
      Date dateBatchFetch
    - dateCached
      
      Date dateCached
    - dateDifferentialAnalysis
      
      Date dateDifferentialAnalysis
    - dateLinkAnalysis
      
      Date dateLinkAnalysis
    - dateMissingValueAnalysis
      
      Date dateMissingValueAnalysis
    - datePcaAnalysis
      
      Date datePcaAnalysis
    - dateProcessedDataVectorComputation
      
      Date dateProcessedDataVectorComputation
    - differentialExpressionAnalyses
      
      Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses
    - expressionExperimentSets
      
      Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> expressionExperimentSets
    - hasBatchInformation
      
      boolean hasBatchInformation
    - hasBothIntensities
      
      Boolean hasBothIntensities
    - hasCoexpressionAnalysis
      
      Boolean hasCoexpressionAnalysis
    - hasDifferentialExpressionAnalysis
      
      Boolean hasDifferentialExpressionAnalysis
    - hasEitherIntensity
      
      Boolean hasEitherIntensity
    - hasMultiplePreferredQuantitationTypes
      
      Boolean hasMultiplePreferredQuantitationTypes
    - hasMultipleTechnologyTypes
      
      Boolean hasMultipleTechnologyTypes
    - isRNASeq
      
      Boolean isRNASeq
    - lastArrayDesignUpdateDate
      
      String lastArrayDesignUpdateDate
    - linkAnalysisEventType
      
      String linkAnalysisEventType
    - missingValueAnalysisEventType
      
      String missingValueAnalysisEventType
    - numAnnotations
      
      Long numAnnotations
    - numPopulatedFactors
      
      Long numPopulatedFactors
    - originalPlatforms
      
      Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> originalPlatforms
    - otherParts
      
      Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> otherParts
    - pcaAnalysisEventType
      
      String pcaAnalysisEventType
    - primaryCitation
      
      ubic.gemma.model.common.description.CitationValueObject primaryCitation
    - processedDataVectorComputationEventType
      
      String processedDataVectorComputationEventType
    - pubmedId
      
      Integer pubmedId
    - QChtml
      
      String QChtml
    - reprocessedFromRawData
      
      boolean reprocessedFromRawData
    - sampleRemovedFlags
      
      Collection<ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject> sampleRemovedFlags
    - secondaryAccession
      
      String secondaryAccession
    - secondaryExternalDatabase
      
      String secondaryExternalDatabase
    - secondaryExternalUri
      
      String secondaryExternalUri
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.analysis.expression.ExpressionExperimentSet> implements Serializable
  
  serialVersionUID:
  
  -6852364688337216390L
  - Serialized Fields
    - description
      
      String description
    - expressionExperimentIds
      
      Collection<Long> expressionExperimentIds
    - isPublic
      
      boolean isPublic
    - modifiable
      
      boolean modifiable
    - name
      
      String name
    - numWithCoexpressionAnalysis
      
      Integer numWithCoexpressionAnalysis
    - numWithDifferentialExpressionAnalysis
      
      Integer numWithDifferentialExpressionAnalysis
    - shared
      
      boolean shared
    - size
      
      Integer size
    - taxonId
      
      Long taxonId
    - taxonName
      
      String taxonName
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet> implements Serializable
  - Serialized Fields
    - accession
      
      String accession
      
      Deprecated.
    - bioAssays
      
      Collection<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> bioAssays
    - characteristics
      
      Collection<ubic.gemma.model.common.description.CharacteristicValueObject> characteristics
    - description
      
      String description
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - minPvalue
      
      Double minPvalue
    - name
      
      String name
    - numberOfBioAssays
      
      Integer numberOfBioAssays
    - sourceExperimentId
      
      Long sourceExperimentId
    - sourceExperimentShortName
      
      String sourceExperimentShortName
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject extends ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<ubic.gemma.model.expression.experiment.ExpressionExperiment> implements Serializable
  
  serialVersionUID:
  
  -6861385216096602508L
  - Serialized Fields
    - accession
      
      String accession
    - arrayDesignCount
      
      Long arrayDesignCount
    - batchConfound
      
      String batchConfound
    - batchEffect
      
      String batchEffect
    - batchEffectStatistics
      
      String batchEffectStatistics
    - bioMaterialCount
      
      Integer bioMaterialCount
    - characteristics
      
      Set<ubic.gemma.model.common.description.CharacteristicValueObject> characteristics
    - description
      
      String description
    - experimentalDesign
      
      Long experimentalDesign
    - externalDatabase
      
      String externalDatabase
    - externalDatabaseUri
      
      String externalDatabaseUri
    - externalUri
      
      String externalUri
    - geeq
      
      ubic.gemma.model.expression.experiment.GeeqValueObject geeq
    - isPublic
      
      boolean isPublic
    - isShared
      
      boolean isShared
    - metadata
      
      String metadata
    - minPvalue
      
      Double minPvalue
    - name
      
      String name
    - numberOfBioAssays
      
      Integer numberOfBioAssays
    - processedExpressionVectorCount
      
      Integer processedExpressionVectorCount
    - shortName
      
      String shortName
    - source
      
      String source
    - suitableForDEA
      
      Boolean suitableForDEA
    - taxonObject
      
      ubic.gemma.model.genome.TaxonValueObject taxonObject
    - technologyType
      
      String technologyType
    - userCanWrite
      
      boolean userCanWrite
    - userOwned
      
      boolean userOwned
- Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject extends ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - value
      
      String value
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FactorValueValueObject extends ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject implements Serializable
  
  serialVersionUID:
  
  3378801249808036785L
  - Serialized Fields
    - category
      
      String category
      
      Deprecated.
    - categoryUri
      
      String categoryUri
      
      Deprecated.
    - charId
      
      Long charId
      
      Deprecated.
    - factorId
      
      Long factorId
      
      Deprecated.
    - needsAttention
      
      Boolean needsAttention
      
      Deprecated.
    - object
      
      String object
      
      Deprecated.
    - objectUri
      
      String objectUri
      
      Deprecated.
    - predicate
      
      String predicate
      
      Deprecated.
    - predicateUri
      
      String predicateUri
      
      Deprecated.
    - secondObject
      
      String secondObject
      
      Deprecated.
    - secondObjectUri
      
      String secondObjectUri
      
      Deprecated.
    - secondPredicate
      
      String secondPredicate
      
      Deprecated.
    - secondPredicateUri
      
      String secondPredicateUri
      
      Deprecated.
    - value
      
      String value
      
      Deprecated.
    - valueUri
      
      String valueUri
      
      Deprecated.
- Class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject extends ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  3557304710219740029L
  - Serialized Fields
    - queryString
      
      String queryString
- Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject extends ubic.gemma.model.expression.experiment.GeeqValueObject implements Serializable
  - Serialized Fields
    - detectedQualityScore
      
      double detectedQualityScore
    - detectedSuitabilityScore
      
      double detectedSuitabilityScore
    - manualBatchConfoundActive
      
      boolean manualBatchConfoundActive
    - manualBatchEffectActive
      
      boolean manualBatchEffectActive
    - manualHasBatchConfound
      
      boolean manualHasBatchConfound
    - manualHasNoBatchEffect
      
      boolean manualHasNoBatchEffect
    - manualHasStrongBatchEffect
      
      boolean manualHasStrongBatchEffect
    - manualQualityOverride
      
      boolean manualQualityOverride
    - manualQualityScore
      
      double manualQualityScore
    - manualSuitabilityOverride
      
      boolean manualSuitabilityOverride
    - manualSuitabilityScore
      
      double manualSuitabilityScore
    - otherIssues
      
      String otherIssues
    - qScoreBatchConfound
      
      double qScoreBatchConfound
    - qScoreBatchEffect
      
      double qScoreBatchEffect
- Class ubic.gemma.model.expression.experiment.GeeqValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.experiment.Geeq> implements Serializable
  - Serialized Fields
    - batchCorrected
      
      boolean batchCorrected
    - corrMatIssues
      
      byte corrMatIssues
    - noVectors
      
      boolean noVectors
    - publicQualityScore
      
      double publicQualityScore
    - publicSuitabilityScore
      
      double publicSuitabilityScore
    - qScoreBatchInfo
      
      double qScoreBatchInfo
    - qScoreOutliers
      
      double qScoreOutliers
    - qScorePlatformsTech
      
      double qScorePlatformsTech
    - qScorePublicBatchConfound
      
      double qScorePublicBatchConfound
    - qScorePublicBatchEffect
      
      double qScorePublicBatchEffect
    - qScoreReplicates
      
      double qScoreReplicates
    - qScoreSampleCorrelationVariance
      
      double qScoreSampleCorrelationVariance
    - qScoreSampleMeanCorrelation
      
      double qScoreSampleMeanCorrelation
    - qScoreSampleMedianCorrelation
      
      double qScoreSampleMedianCorrelation
    - replicatesIssues
      
      byte replicatesIssues
    - sScoreAvgPlatformPopularity
      
      double sScoreAvgPlatformPopularity
    - sScoreAvgPlatformSize
      
      double sScoreAvgPlatformSize
    - sScoreMissingValues
      
      double sScoreMissingValues
    - sScorePlatformAmount
      
      double sScorePlatformAmount
    - sScorePlatformsTechMulti
      
      double sScorePlatformsTechMulti
    - sScorePublication
      
      double sScorePublication
    - sScoreRawData
      
      double sScoreRawData
    - sScoreSampleSize
      
      double sScoreSampleSize
- Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject implements Serializable
  
  serialVersionUID:
  
  2068650886972222818L
  - Serialized Fields
    - modified
      
      boolean modified
- Class ubic.gemma.model.expression.experiment.StatementValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.expression.experiment.Statement> implements Serializable
  - Serialized Fields
    - category
      
      String category
    - categoryUri
      
      String categoryUri
    - object
      
      String object
    - objectId
      
      String objectId
    - objectUri
      
      String objectUri
    - predicate
      
      String predicate
    - predicateUri
      
      String predicateUri
    - secondObject
      
      String secondObject
    - secondObjectUri
      
      String secondObjectUri
    - secondPredicate
      
      String secondPredicate
    - secondPredicateUri
      
      String secondPredicateUri
    - subject
      
      String subject
    - subjectId
      
      String subjectId
    - subjectUri
      
      String subjectUri
Package ubic.gemma.model.genome
- Class ubic.gemma.model.genome.GeneOntologyTermValueObject extends Object implements Serializable
  - Serialized Fields
    - comment
      
      String comment
    - goId
      
      String goId
    - isObsolete
      
      boolean isObsolete
    - label
      
      String label
    - localName
      
      String localName
    - term
      
      String term
    - uri
      
      String uri
- Class ubic.gemma.model.genome.PhysicalLocationValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.genome.PhysicalLocation> implements Serializable
  - Serialized Fields
    - bin
      
      Integer bin
    - chromosome
      
      String chromosome
    - nucleotide
      
      Long nucleotide
    - nucleotideLength
      
      Integer nucleotideLength
    - strand
      
      String strand
    - taxon
      
      ubic.gemma.model.genome.TaxonValueObject taxon
- Class ubic.gemma.model.genome.TaxonValueObject extends ubic.gemma.model.common.IdentifiableValueObject<ubic.gemma.model.genome.Taxon> implements Serializable
  - Serialized Fields
    - commonName
      
      String commonName
    - externalDatabase
      
      ubic.gemma.model.common.description.ExternalDatabaseValueObject externalDatabase
    - isGenesUsable
      
      Boolean isGenesUsable
    - isSpecies
      
      Boolean isSpecies
    - ncbiId
      
      Integer ncbiId
    - scientificName
      
      String scientificName
Package ubic.gemma.persistence.hibernate
- Class ubic.gemma.persistence.hibernate.HibernateTransactionManager extends org.springframework.orm.hibernate4.HibernateTransactionManager implements Serializable
- Class ubic.gemma.persistence.hibernate.LocalSessionFactoryBuilder extends org.springframework.orm.hibernate4.LocalSessionFactoryBuilder implements Serializable
- Class ubic.gemma.persistence.hibernate.XSDEntityResolver extends DTDEntityResolver implements Serializable
Package ubic.gemma.persistence.service
- Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage extends Exception implements Serializable
- Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage extends Exception implements Serializable
Package ubic.gemma.persistence.service.analysis.expression.diff
- Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult extends ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  -2868418055346274525L
- Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult extends ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult implements Serializable
  
  serialVersionUID:
  
  3501605965895623139L
Package ubic.gemma.persistence.service.association.coexpression
- Class ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  184287422449009209L
  - Serialized Fields
    - coexGeneSymbol
      
      String coexGeneSymbol
    - coexpGene
      
      Long coexpGene
    - positiveCorrelation
      
      boolean positiveCorrelation
    - queryGene
      
      Long queryGene
    - queryGeneSymbol
      
      String queryGeneSymbol
    - support
      
      int support
    - supportDetailsId
      
      Long supportDetailsId
    - supportingDatasets
      
      Collection<Long> supportingDatasets
    - testedInDatasets
      
      ubic.gemma.persistence.service.association.coexpression.CompressedLongSet testedInDatasets
- Class ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject extends Object implements Serializable
  - Serialized Fields
    - coexGeneId
      
      Long coexGeneId
    - coexGeneSymbol
      
      String coexGeneSymbol
    - eeConstraint
      
      boolean eeConstraint
    - fromCache
      
      boolean fromCache
    - interQueryLink
      
      boolean interQueryLink
    - maxResults
      
      int maxResults
    - positiveCorrelation
      
      boolean positiveCorrelation
    - queryGeneId
      
      Long queryGeneId
    - queryGeneSymbol
      
      String queryGeneSymbol
    - queryStringency
      
      int queryStringency
    - support
      
      Integer support
    - supportDetailsId
      
      Long supportDetailsId
    - supportingDatasets
      
      Set<Long> supportingDatasets
    - testedInDatasets
      
      Set<Long> testedInDatasets
Package ubic.gemma.persistence.service.common.quantitationtype
- Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException extends Exception implements Serializable
Package ubic.gemma.persistence.service.expression.bioAssayData
- Class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution extends org.apache.commons.math3.distribution.AbstractIntegerDistribution implements Serializable
  - Serialized Fields
    - distribution
      
      NegativeBinomial distribution
    - i
      
      int i
    - v
      
      double v
Package ubic.gemma.persistence.service.expression.experiment
- Class ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException extends RuntimeException implements Serializable
  - Serialized Fields
    - migration
      
      ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.Migration migration
Package ubic.gemma.persistence.service.maintenance
- Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus extends Object implements Serializable
  
  serialVersionUID:
  
  1956861185764899312L
  - Serialized Fields
    - annotation
      
      String annotation
    - error
      
      Exception error
    - lastUpdate
      
      Date lastUpdate
Package ubic.gemma.rest
- Class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject extends ubic.gemma.model.common.description.AnnotationValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
    - parentTerms
      
      Set<ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject> parentTerms
- Class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject extends ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperimentsForTechnologyType
      
      Long numberOfExpressionExperimentsForTechnologyType
- Class ubic.gemma.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject extends ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject implements Serializable
  - Serialized Fields
    - baseline
      
      ubic.gemma.model.expression.experiment.FactorValueBasicValueObject baseline
    - experimentAnalyzedId
      
      Long experimentAnalyzedId
    - resultSetId
      
      Long resultSetId
    - secondBaseline
      
      ubic.gemma.model.expression.experiment.FactorValueBasicValueObject secondBaseline
    - sourceExperimentId
      
      Long sourceExperimentId
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject implements Serializable
  - Serialized Fields
    - factorValues
      
      List<ubic.gemma.model.expression.experiment.FactorValueBasicValueObject> factorValues
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject implements Serializable
  - Serialized Fields
    - subSetGroupIds
      
      List<Long> subSetGroupIds
- Class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject implements Serializable
  - Serialized Fields
    - searchResult
      
      ubic.gemma.rest.SearchWebService.SearchResultValueObject<ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject> searchResult
- Class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject extends ubic.gemma.model.genome.TaxonValueObject implements Serializable
  - Serialized Fields
    - numberOfExpressionExperiments
      
      Long numberOfExpressionExperiments
Package ubic.gemma.rest.serializers
- Class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<T extends ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer extends ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer<ubic.gemma.model.expression.experiment.FactorValueBasicValueObject> implements Serializable
- Class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer extends ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer<ubic.gemma.model.expression.experiment.FactorValueValueObject> implements Serializable
Package ubic.gemma.rest.util
- Class ubic.gemma.rest.util.EntityNotFoundException extends Exception implements Serializable
- Class ubic.gemma.rest.util.MalformedArgException extends javax.ws.rs.BadRequestException implements Serializable
Package ubic.gemma.web.controller.common.auditAndSecurity
- Class ubic.gemma.web.controller.common.auditAndSecurity.FileUpload extends Object implements Serializable
  
  serialVersionUID:
  
  537156568346654834L
  - Serialized Fields
    - file
      
      byte[] file
    - localPath
      
      String localPath
- Class ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - authority
      
      String authority
    - principal
      
      boolean principal
Package ubic.gemma.web.controller.common.auditAndSecurity.recaptcha
- Class ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException extends RuntimeException implements Serializable

Package ubic.gemma.web.controller.expression.arrayDesign

Class ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt extends ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject implements Serializable

serialVersionUID:: 218696698777199533L

Serialized Fields

additionalTaxa
```
Set<String> additionalTaxa
```
allParentsAnnotationLink
```
String allParentsAnnotationLink
```
alternateNames
```
Collection<String> alternateNames
```

alternative

ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject alternative

bioProcessAnnotationLink
```
String bioProcessAnnotationLink
```
colorString
```
String colorString
```

mergees

Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> mergees

merger

ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject merger

noParentsAnnotationLink
```
String noParentsAnnotationLink
```

subsumees

Collection<ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject> subsumees

subsumer

ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject subsumer

Package ubic.gemma.web.controller.expression.experiment
- Class ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - count
      
      int count
    - factors
      
      List<String> factors
    - factorTypes
      
      List<String> factorTypes
    - factorValueMap
      
      Map<String,String> factorValueMap
- Class ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject extends ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject implements Serializable
  - Serialized Fields
    - bioMaterialCharacteristicCategoryToUse
      
      String bioMaterialCharacteristicCategoryToUse
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand extends ubic.gemma.core.job.TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - analysisId
      
      Long analysisId
    - experimentalDesignId
      
      Long experimentalDesignId
    - expressionExperimentId
      
      Long expressionExperimentId
    - filter
      
      boolean filter
    - forceRewrite
      
      boolean forceRewrite
    - format
      
      String format
    - quantitationTypeId
      
      Long quantitationTypeId
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject extends ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject implements Serializable
  
  serialVersionUID:
  
  1630521876359566915L
  - Serialized Fields
    - bioAssays
      
      Collection<ubic.gemma.model.expression.bioAssay.BioAssayValueObject> bioAssays
    - quantitationTypes
      
      Collection<ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject> quantitationTypes
- Class ubic.gemma.web.controller.expression.experiment.ExpressionExperimentUploadResponse extends Object implements Serializable
  - Serialized Fields
    - error
      
      boolean error
    - errorMessage
      
      String errorMessage
    - taskId
      
      Long taskId
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation extends Object implements Serializable
  - Serialized Fields
    - arrayDesignMatchesDataFile
      
      boolean arrayDesignMatchesDataFile
    - arrayDesignMismatchProblemMessage
      
      String arrayDesignMismatchProblemMessage
    - dataFileFormatProblemMessage
      
      String dataFileFormatProblemMessage
    - dataFileIsValidFormat
      
      boolean dataFileIsValidFormat
    - isValid
      
      boolean isValid
    - nonMatchingProbeNameExamples
      
      Collection<String> nonMatchingProbeNameExamples
    - numberMatchingProbes
      
      int numberMatchingProbes
    - numberOfNonMatchingProbes
      
      int numberOfNonMatchingProbes
    - numColumns
      
      int numColumns
    - numRows
      
      int numRows
    - otherProblemsMessage
      
      String otherProblemsMessage
    - quantitationTypeIsValid
      
      boolean quantitationTypeIsValid
    - quantitationTypeProblemMessage
      
      String quantitationTypeProblemMessage
    - shortNameIsUnique
      
      boolean shortNameIsUnique
- Class ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand extends ubic.gemma.core.job.TaskCommand implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayDesignIds
      
      Collection<Long> arrayDesignIds
    - description
      
      String description
    - isRatio
      
      Boolean isRatio
    - name
      
      String name
    - originalFileName
      
      String originalFileName
    - pubMedId
      
      Integer pubMedId
    - quantitationTypeDescription
      
      String quantitationTypeDescription
    - quantitationTypeName
      
      String quantitationTypeName
    - scale
      
      ubic.gemma.model.common.quantitationtype.ScaleType scale
    - serverFilePath
      
      String serverFilePath
    - shortName
      
      String shortName
    - taxonId
      
      Long taxonId
    - validateOnly
      
      boolean validateOnly
Package ubic.gemma.web.controller.job
- Class ubic.gemma.web.controller.job.SubmittedTaskValueObject extends Object implements Serializable
  
  serialVersionUID:
  
  6757089319713433356L
  - Serialized Fields
    - done
      
      boolean done
    - emailAlert
      
      boolean emailAlert
    - finishTime
      
      Date finishTime
    - lastLogMessage
      
      String lastLogMessage
    - logMessages
      
      String logMessages
    - runningRemotely
      
      boolean runningRemotely
    - startTime
      
      Date startTime
    - submissionTime
      
      Date submissionTime
    - submitter
      
      String submitter
    - taskId
      
      String taskId
    - taskStatus
      
      String taskStatus
    - taskType
      
      String taskType

Serialized Form

Package ubic.gemma.core.analysis.expression.coexpression.links

Class ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig extends Object implements Serializable

Serialized Fields

absoluteValue

arrayName

cdfCut

checkCorrelationDistribution

checkForBatchEffect

checkForOutliers

correlationCacheThreshold

fwe

lowerCdfCutUsed

lowerTailCut

makeSampleCorrMatImages

metric

minNumPresent

normalizationMethod

omitNegLinks

outputFile

probeDegreeThreshold

singularThreshold

subset

subsetSize

subsetUsed

textOut

upperCdfCutUsed

upperTailCut

useDb

Class ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException extends RuntimeException implements Serializable

Package ubic.gemma.core.analysis.expression.diff

Class ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable

Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException extends ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException implements Serializable

Class ubic.gemma.core.analysis.expression.diff.AnalysisException extends RuntimeException implements Serializable

Serialized Fields

config

Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable

Serialized Fields

activeExperiments

fisherPValue

gene

numExperimentsInScope

numMetThreshold

numSearchedExperiments

probeResults

sortKey

Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand extends Object implements Serializable

Serialized Fields

eeId

efId

Class ubic.gemma.core.analysis.expression.diff.EbayesFailureException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable

Class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable

Class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable

Class ubic.gemma.core.analysis.expression.diff.NoSampleLeftForAnalysisException extends ubic.gemma.core.analysis.expression.diff.AnalysisException implements Serializable

Package ubic.gemma.core.analysis.preprocess

Class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable

Serialized Fields

cause

Class ubic.gemma.core.analysis.preprocess.InsufficientProbesException extends ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException implements Serializable

Class ubic.gemma.core.analysis.preprocess.PreprocessingException extends RuntimeException implements Serializable

Class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable

Serialized Fields

cause

Class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable

Serialized Fields

cause

Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable

Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException extends ubic.gemma.core.analysis.preprocess.PreprocessingException implements Serializable

Serialized Fields

cause

Package ubic.gemma.core.analysis.preprocess.batcheffects

Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound extends Object implements Serializable

Serialized Fields

chiSquare

df

ee

ef

numBatches

p

Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException extends ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException implements Serializable