Interface SVDServiceHelper
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- All Known Implementing Classes:
SVDServiceHelperImpl
public interface SVDServiceHelper
Performs Singular value decomposition on experiment data to get eigengenes, and does comparison of those PCs to factors recorded in the experimental design.- Author:
- paul
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Set<ExperimentalFactor>
getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Map<ProbeLoading,DoubleVectorValueObject>
getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
boolean
hasPca(ExpressionExperiment ee)
SVDValueObject
retrieveSvd(ExpressionExperiment ee)
SVDValueObject
svd(ExpressionExperiment ee)
SVDValueObject
svdFactorAnalysis(PrincipalComponentAnalysis pca)
Compare ExperimentalFactors and BioAssay.processingDates to the PCs.SVDValueObject
svdFactorAnalysis(ExpressionExperiment ee)
Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
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Method Detail
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retrieveSvd
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) SVDValueObject retrieveSvd(ExpressionExperiment ee)
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svd
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) SVDValueObject svd(ExpressionExperiment ee) throws SVDException
- Throws:
SVDException
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getTopLoadedVectors
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Map<ProbeLoading,DoubleVectorValueObject> getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
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hasPca
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) boolean hasPca(ExpressionExperiment ee)
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getImportantFactors
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Set<ExperimentalFactor> getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
- Parameters:
experimentalFactors
- to considerimportanceThreshold
- threshold for pvalue of association with factor. Suggested value might be 0.01.ee
- the expression experiment- Returns:
- factors which are "significantly" associated with one of the first three PCs
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svdFactorAnalysis
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) SVDValueObject svdFactorAnalysis(PrincipalComponentAnalysis pca)
Compare ExperimentalFactors and BioAssay.processingDates to the PCs.- Parameters:
pca
- PCA- Returns:
- SVD VO
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svdFactorAnalysis
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) SVDValueObject svdFactorAnalysis(ExpressionExperiment ee)
Compare ExperimentalFactors and BioAssay.processingDates to the PCs.- Parameters:
ee
- the experiment- Returns:
- SVD VO
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