Package ubic.gemma.core.analysis.expression.diff
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Interface Summary Interface Description DifferentialExpressionAnalysisHelperService Service methods to do database-related work for differential expression analysisDifferentialExpressionAnalyzerService DiffExAnalyzer DiffExMetaAnalyzerService Used to perform meta-analyses of complete data sets (actually result sets), select the top genes, and potentially store the results.GeneDifferentialExpressionService GeneDiffExMetaAnalysisHelperService -
Class Summary Class Description BaselineSelection Utilities for deciding if a factor value is a baseline condition.DifferentialExpressionAnalysisConfig Holds the settings used for differential expression analysis, and defines some defaults.DifferentialExpressionAnalysisHelperServiceImpl Transactional methods for dealing with differential expression analyses.DifferentialExpressionAnalysisUtil A helper class for the differential expression analyzers.DifferentialExpressionAnalyzerServiceImpl Differential expression service to run the differential expression analysis (and persist the results using the appropriate data access objects).DifferentialExpressionFileUtils DifferentialExpressionMetaAnalysisValueObject A value object with meta analysis results.DiffExAnalyzerUtils DiffExMetaAnalyzerServiceImpl DiffExpressionSelectedFactorCommand A command object with a selected factor and associated experiment.GeneDifferentialExpressionServiceImpl Provides access toDifferentialExpressionAnalysisResults and meta-analysis results.GeneDiffExMetaAnalysisHelperServiceImpl * @author francesLinearModelAnalyzer Handles fitting linear models with continuous or fixed-level covariates. -
Enum Summary Enum Description AnalysisType Defines the different types of analyses our linear modeling framework supports: GENERICLM - generic linear regression (interactions are omitted, but this could change) OSTTEST - one sample t-test OWA - one-way ANOVA TTEST - two sample t-test TWO_WAY_ANOVA_WITH_INTERACTION TWO_WAY_ANOVA_NO_INTERACTION -
Exception Summary Exception Description AllSubSetAnalysesFailedException Exception raised when all subset analyses failed with anAnalysisException.AnalysisException Base exception for all differential analysis-related exceptions.EbayesFailureException Occurs when empirical bayes estimation fails.InvalidQuantitationTypeConversionException Exception raised when a log2 conversion fails.NoFactorLeftForAnalysisException Exception raised when suitable factor is left for analysis.NoSampleLeftForAnalysisException Exception raised when no sample is left for analysis.