Package ubic.gemma.core.analysis.preprocess.batcheffects

Interface ExpressionExperimentBatchCorrectionService

All Known Implementing Classes:
ExpressionExperimentBatchCorrectionServiceImpl
public interface ExpressionExperimentBatchCorrectionService
Author:
Paul

  • Method Details

    • checkCorrectability

      boolean checkCorrectability(ExpressionExperiment ee)
      Is there a Batch factor provided? Is there a confound problem? Do we have at least two samples per batch? This will return true even if there is evidence the data has been batch-corrected before; we assume the caller wants to redo it based on the raw data
      Parameters:
      ee - the experiment
      Returns:
      whether it is correctable

    • comBat

      @Nullable ExpressionDataDoubleMatrix comBat(ExpressionExperiment ee)
      Run ComBat using default settings (parametric)

      The matrix is constructed from the experiment's processed vectors.

    • comBat

      @Nullable ExpressionDataDoubleMatrix comBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix mat)
      Run ComBat with a specific data matrix.
      Parameters:
      mat - the matrix
      Returns:
      batch corrected matrix, or null if there's no batching factor

    • getBatchFactor

      @Nullable ExperimentalFactor getBatchFactor(ExpressionExperiment ee)
      For convenience of some testing classes
      Parameters:
      ee - the experiment to get the batch factor for
      Returns:
      the batch factor of the experiment, or null, if experiment has no batch factor