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

Interface ExpressionExperimentBatchInformationService

All Known Implementing Classes:
ExpressionExperimentBatchInformationServiceImpl
public interface ExpressionExperimentBatchInformationService
Provides status of batch information for datasets.

  • Method Details

    • checkHasBatchInfo

      boolean checkHasBatchInfo(ExpressionExperiment ee)
      Check if the given experiment has batch information.

      This does not imply that the batch information is usable or valid. Use checkHasUsableBatchInfo(ExpressionExperiment) for that purpose.

    • checkHasUsableBatchInfo

      boolean checkHasUsableBatchInfo(ExpressionExperiment ee)
      Check if the given experiment has usable batch information.

    • hasSignificantBatchConfound

      boolean hasSignificantBatchConfound(ExpressionExperiment ee)
      Check if a given experiment has a significant batch confound.

    • getSignificantBatchConfounds

      List<BatchConfound> getSignificantBatchConfounds(ExpressionExperiment ee)
      Obtain the significant batch confounds for a dataset.

    • getSignificantBatchConfoundsForSubsets

      Map<ExpressionExperimentSubSet,List<BatchConfound>> getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)
      Obtain the significant batch confounds for a dataset subsets.

    • getBatchConfoundAsHtmlString

      @Nullable String getBatchConfoundAsHtmlString(ExpressionExperiment ee)
      Summarize the batch confounds for a given dataset or its subsets in an HTML string.
      Returns:
      a summary or null if there is no batch confound

    • getBatchEffectDetails

      BatchEffectDetails getBatchEffectDetails(ExpressionExperiment ee)
      Obtain the full batch effect details of a given experiment.
      Parameters:
      ee - experiment
      Returns:
      details for the principal component most associated with batches (even if it isn't "significant"). Note that we don't look at every component, just the first few.