Package ubic.gemma.core.analysis.preprocess
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Interface Summary Interface Description MeanVarianceService Responsible for returning the coordinates of the experiment's Mean-Variance relationship.MeanVarianceServiceHelper OutlierDetectionService PreprocessorService Encapsulates steps that are done to expression data sets after they are loaded and experimental design curated.SplitExperimentService TODO Document MeTwoChannelMissingValueHelperService TwoChannelMissingValues VectorMergingService -
Class Summary Class Description ExpressionDataMatrixBuilder Utility methods for taking an ExpressionExperiment and returning various types of ExpressionDataMatrices, such as the processed data, preferred data, background, etc.MeanVarianceServiceImpl Manage the mean-variance relationship.OutlierDetails Container for details about a proposed outlierOutlierDetectionServiceImpl Methods to (attempt to) detect outliers in data sets.PreprocessorServiceImpl SplitExperimentServiceImpl Split an experiment into multiple experiments.TwoChannelMissingValuesImpl Computes a missing value matrix for ratiometric data sets.VectorMergingServiceImpl Tackles the problem of concatenating DesignElementDataVectors for a single experiment. -
Exception Summary Exception Description FailedToComputeSingularValueDecomposition InsufficientProbesException PreprocessingException Allows us to catch preprocessing errors and handle them correctly.QuantitationMismatchPreprocessingException SampleCoexpressionRelatedPreprocessingException Exception raised in preprocessing when there is a problem with sample coexpression analysis.SVDRelatedPreprocessingException Exception raised if a SVD cannot be computed.UnsupportedQuantitationScaleConversionException Exception raised when data from a given scale cannot be converted to another scale.