Package ubic.gemma.core.analysis.preprocess
@ParametersAreNonnullByDefault
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.Encapsulates steps that are done to expression data sets after they are loaded and experimental design curated.An exception that wraps a
QuantitationTypeDetectionException.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.Computes a missing value matrix for ratiometric data sets.Tackles the problem of concatenating DesignElementDataVectors for a single experiment.