Class DifferentialExpressionAnalysisResult

java.lang.Object
ubic.gemma.model.analysis.AnalysisResult
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
All Implemented Interfaces:
Identifiable
@Entity public class DifferentialExpressionAnalysisResult extends AnalysisResult
Result of an analysis of differences in expression levels -- a single test (e.g., for one gene or one probe), for one factor. These statistics are based on ANOVA-style analysis, with a collection of ContrastResults storing the associated contrasts.

Intentionally no @Cache on this entity or its contrasts bag. This is the inner level of the two-level ExpressionAnalysisResultSet -> DifferentialExpressionAnalysisResult chain flagged by HIBERNATE6_CASCADE_AUDIT.md risk #3 (matches the AuditTrail/AuditEvent shape fixed in ab8b4c443c): a read-only L2 cache on a mutable="false" child of a mutable="false" parent causes Hibernate 6 to serve stale empty-bag results to fresh-session reads after cross-tx writes. @Immutable is retained because the rows ARE write-once-immutable; do not re-add an L2 cache directive without first re-validating the audit's read-path scenario.

  • Constructor Details

    • DifferentialExpressionAnalysisResult

      public DifferentialExpressionAnalysisResult()

  • Method Details

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getContrasts

      public Set<ContrastResult> getContrasts()
      Returns:
      Contrasts for this result. Depending on configuration, this might only be stored if the Result itself is significant at some given threshold (e.g., nominal p-value of 0.05) (but default is to store everything)

    • setContrasts

      public void setContrasts(Set<ContrastResult> contrasts)

    • getCorrectedPvalue

      @Nullable public Double getCorrectedPvalue()
      Returns:
      A false discovery estimate (qvalue)

    • setCorrectedPvalue

      public void setCorrectedPvalue(@Nullable Double correctedPvalue)

    • getCorrectedPValueBin

      @Nullable public Integer getCorrectedPValueBin()
      Returns:
      an indexable parameter for the corrected qvalue, to speed searches.

    • setCorrectedPValueBin

      public void setCorrectedPValueBin(@Nullable Integer correctedPValueBin)

    • getId

      public Long getId()
      Description copied from interface: Identifiable
      Obtain the identifier of the object.

    • setId

      public void setId(Long id)

    • getProbe

      public CompositeSequence getProbe()

    • setProbe

      public void setProbe(CompositeSequence probe)

    • getPvalue

      @Nullable public Double getPvalue()
      Returns:
      The p-value from the test for rejection of the null hypothesis of no effect

    • setPvalue

      public void setPvalue(@Nullable Double pvalue)

    • getRank

      @Nullable public Double getRank()
      Returns:
      The fractional rank of this result, relative to the others in the ResultSet. Thus the best (lowest p-value) will have a fractional rank of 0.0, the worst wil lbe 1.0.

    • setRank

      public void setRank(@Nullable Double rank)

    • getResultSet

      public ExpressionAnalysisResultSet getResultSet()

    • setResultSet

      public void setResultSet(ExpressionAnalysisResultSet resultSet)