Package ubic.gemma.core.analysis.expression.diff
@NonNullApi
package ubic.gemma.core.analysis.expression.diff
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ClassesClassDescriptionUnit tests for the differential-expression analysis exception family:
AnalysisException(base) and its sub-types (MeanVarianceFailureException).Which existing analyses a newly persisted one replaces.Deleting an analysis waits for the archive write that saving it scheduled.A fresh run withdeleteOtherAnalysessaves its analyses first, then deletes the experiment's other analyses on the same subset factor.A redo keeps the old replacement rule: only an analysis on the identical factor set is replaced.Unit tests for the R-friendly name helpers inDiffExAnalyzerUtils+ the interaction-term formatter.Samples marked DE_Exclude and samples whose assays are flagged as outliers must leave the analysis before anything is decided from the sample set.Pure-mock unit test forDiffExGeneWarmupService.This is a test that requires complex setup: loading several data sets, information on genes, array design annotations, conducting differential expression, and finally the meta-analysis.Tests added to check various cases of differential expression analysis.for bug 3927An arm of the subset factor that no analyzed sample carries is skipped, not a fatal condition for the experiment.A factor dropped for missing values must not be left behind in the baseline map.Test based on GSE19480, see bug 3177Producing no analysis at all is a failure of the experiment, not a quiet empty result.This test covers subset analysis with pre-existing EE subset structure.A subset analysis has to describe itself with the factors it actually modelled.Test based on GSE8441