Class ExpressionExperimentBatchCorrectionServiceImplTest

java.lang.Object
ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImplTest
public class ExpressionExperimentBatchCorrectionServiceImplTest extends Object
Unit tests for ExpressionExperimentBatchCorrectionServiceImpl that need no Spring context: the comBat(ee, matrix) path only reads the experiment's in-memory design, so the impl can be constructed directly.
Author:
paul

  • Constructor Details

    • ExpressionExperimentBatchCorrectionServiceImplTest

      public ExpressionExperimentBatchCorrectionServiceImplTest()

  • Method Details

    • setUp

      @BeforeEach public void setUp()

    • testComBat

      @Test public void testComBat()

    • testComBatWithAnOutlier

      @Test public void testComBatWithAnOutlier()
      Outlier samples are sliced out before ComBat runs and their original values put back afterwards. The restored matrix still has to carry ComBat's quantitation type: PreprocessorHelperServiceImpl.getCorrectedData checks isBatchCorrected on the way out and throws if it is unset, so returning the original matrix as-is fails every experiment that has an outlier.