[BioC] GSEAlm Help

Masood-Ul-Hassan M.Zaka at student.bradford.ac.uk
Tue Apr 3 14:45:15 CEST 2012


I am having gsnnormalize error during pval calculation. I am pasting my eset below,  could you please advise me if there is problem with the "eset" and if there is do i need to subset the phenodata to get some sort of solution. Thanks

M Zaka

Phd Student of Bioinformatics
University of Bradford, UK

pVals = gsealmPerm(eset, ~disease.state, mSigDB, nperm = 1000)
Error in GSNormalize(obsRaw$tstat[2, ], incidence = mat, ...) : 
  GSNormalize: non-conforming matrices

ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 36 samples 
  element names: exprs 
protocolData: none
  sampleNames: GSM512539 GSM512540 ... GSM512565 (36 total)
  varLabels: sample specimen disease.state description
  varMetadata: labelDescription
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283
  fvarLabels: ID Gene title ... GO:Component ID (21 total)
  fvarMetadata: Column labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 20197764 

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