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)
      Check if the given experiment is correctable for batch effects.

      For a dataset to be correctable, it must meet the following criteria:

      • a batch factor must be present
      • there must be no confounding factor
      • there must be 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