Package ubic.gemma.core.analysis.preprocess
@NonNullApi
package ubic.gemma.core.analysis.preprocess
This package contains classes for preprocessing expression data.
By preprocessing, we mean all the steps necessary to get data ready for analysis in the form of a set of
ProcessedExpressionDataVector from a set of
RawExpressionDataVector.
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ClassDescriptionResponsible for returning the coordinates of the experiment's Mean-Variance relationship.Manage the mean-variance relationship.Container for details about a proposed outlier.Methods to (attempt to) detect outliers in data sets.Allows us to catch preprocessing errors and handle them correctly.Co-bean carrying the
processFor*diagnostic steps thatPreprocessorServiceImpl.processDiagnostics(ExpressionExperiment)runs as part of the post-load preprocessing pipeline.Implementation ofPreprocessorHelperService: a thin co-bean that exists so eachprocessFor*method is invoked through a Spring proxy and theAuditedOnErroraspect can intercept its catch path.Encapsulates steps that are done to expression data sets after they are loaded and experimental design curated.An exception that wraps aQuantitationTypeDetectionException.Exception raised in preprocessing when there is a problem with sample coexpression analysis.TODO Document MeSplit an experiment into multiple experiments.Exception raised if a SVD cannot be computed.Deprecated.Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.Deprecated.Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.Deprecated.Two-colour arrays are no longer supported for new data; kept so existing two-colour datasets still load and reprocess.Tackles the problem of concatenating DesignElementDataVectors for a single experiment.