Class BatchConfoundUtilsTest

java.lang.Object
ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtilsTest
public class BatchConfoundUtilsTest extends Object
Unit tests for BatchConfoundUtils, covering biomaterials that carry no value for a factor.

These are built entirely from transient entities: BatchConfoundUtils.test(BioAssaySet) reads only the bioassays, their samples and those samples' factor values, so no persistence is involved.

Author:
gembro

  • Constructor Details

    • BatchConfoundUtilsTest

      public BatchConfoundUtilsTest()

  • Method Details

    • continuousFactorWithAMissingValueExcludesThatSample

      @Test public void continuousFactorWithAMissingValueExcludesThatSample()
      A batch factor confounded with a continuous factor, where one sample has no value for that factor.

      getBioMaterialFactorMap() pads every factor's map with a null for each sample that has no value for it, and the Kruskal-Wallis leg used to unbox that null.

    • continuousFactorWithTooFewUsableSamplesIsSkipped

      @Test public void continuousFactorWithTooFewUsableSamplesIsSkipped()
      Once samples with no value are excluded, too few may be left to rank.

    • factorCategoryWithNoValueIsTolerated

      @Test public void factorCategoryWithNoValueIsTolerated()
      A factor whose category carries no value. Characteristic.getValue() is nullable and is null for 8,165 production rows.