Package ubic.gemma.core.analysis.preprocess.svd

Interface SVDService

All Known Implementing Classes:

SVDServiceImpl

public interface SVDService

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

Method Summary

Modifier and Type	Method	Description
Set<ExperimentalFactor>	getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
SVDResult	getSvd(ExpressionExperiment ee)
SVDResult	getSvdFactorAnalysis(PrincipalComponentAnalysis pca)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
SVDResult	getSvdFactorAnalysis(ExpressionExperiment ee)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
Map<ProbeLoading,DoubleVectorValueObject>	getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
boolean	hasPca(ExpressionExperiment ee)
SVDResult	svd(ExpressionExperiment ee)

Method Detail

getTopLoadedVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<ProbeLoading,DoubleVectorValueObject> getTopLoadedVectors(ExpressionExperiment ee,
                                                                    int component,
                                                                    int count)

hasPca

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
boolean hasPca(ExpressionExperiment ee)

getSvd

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SVDResult getSvd(ExpressionExperiment ee)

svd

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
SVDResult svd(ExpressionExperiment ee)
       throws SVDException

Throws:

SVDException

getSvdFactorAnalysis

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SVDResult getSvdFactorAnalysis(ExpressionExperiment ee)

Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Parameters:

ee - the experiment

Returns:

SVD VO

getSvdFactorAnalysis

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SVDResult getSvdFactorAnalysis(PrincipalComponentAnalysis pca)

Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Parameters:

pca - PCA

Returns:

SVD VO

getImportantFactors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Set<ExperimentalFactor> getImportantFactors(ExpressionExperiment ee,
                                            Collection<ExperimentalFactor> experimentalFactors,
                                            Double importanceThreshold)

Parameters:

experimentalFactors - to consider

importanceThreshold - 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