Package ubic.gemma.core.analysis.expression.diff

Interface GeneDifferentialExpressionService

All Known Implementing Classes:
GeneDifferentialExpressionServiceImpl
public interface GeneDifferentialExpressionService
Author:
paul

  • Field Details

    • PVALUE_CLIP_THRESHOLD

      static final double PVALUE_CLIP_THRESHOLD
      p values smaller than this will be treated as this value in a meta-analysis. The reason is to avoid extremely low pvalues from driving meta-pvalues down too fast. This is suggested by the fact that very small pvalues presume an extremely high precision in agreement between the tails of the true null distribution and the analytic distribution used to compute the pvalues (e.g., F or t).
      See Also:

  • Method Details

    • configExperimentalFactorValueObject

      ExperimentalFactorValueObject configExperimentalFactorValueObject(ExperimentalFactor ef)

    • getDifferentialExpression

      Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, Collection<BioAssaySet> experimentsAnalyzed, boolean includeSubSets)
      Get the differential expression results for the given gene that is in a specified set of experiments.
      Parameters:
      gene - gene of interest
      experimentsAnalyzed - set of experiments or subsets to search
      includeSubSets - include subsets of the experiments analyzed
      Returns:
      DEA VOs

    • getDifferentialExpression

      Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, BioAssaySet experimentAnalyzed, boolean includeSubSets, double threshold, int limit)
      Get the differential expression results for the given gene that is in a specified set of experiments.
      Parameters:
      gene - gene of interest
      experimentAnalyzed - set of experiments to search
      includeSubSets - include subsets of the experiment analyzed
      threshold - the cutoff to determine if diff expressed
      limit - the maximum number of results to return (null for all)
      Returns:
      DEA VOs

    • getDifferentialExpression

      Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)
      Get differential expression for a gene, constrained to a specific set of factors. Note that interactions are ignored, only main effects (the factorMap can only have one factor per experiment)
      Parameters:
      gene - gene
      threshold - threshold
      factorMap - factor map
      Returns:
      DEA VOs

    • getDifferentialExpression

      Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, double threshold, int limit)
      Get the differential expression results for the given gene across all datasets.
      Parameters:
      gene - gene
      threshold - threshold
      limit - limit
      Returns:
      DEA VOs

    • getDifferentialExpressionMetaAnalysis

      DifferentialExpressionMetaAnalysisValueObject getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments, boolean includeSubSets)
      Get the differential expression analysis results for the gene in the activeExperiments.
      Parameters:
      threshold - threshold
      g - gene
      eeFactorsMap - factor map
      activeExperiments - active ees
      includeSubSets -
      Returns:
      diff exp. analysis meta VO