blood deconvolution - cellmix
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Entering edit mode
5.6 years ago
kuragari.ch ▴ 20

Dear all,

 

I want to perform the deconvolution of a set of blood samples (microarray). Hence I tried to use CellMix. Beeing tapas2 my data-set:

R> tapas2
ExpressionSet (storageMode: lockedEnvironment)
assayData: 11054 features, 112 samples
  element names: exprs
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu133a.db
R> exprs(tapas2)[1:3, 1:3]
              7233105     7340906     7421905
206797_at -0.29448977 -0.07602026  0.51537574
204639_at -0.06513502 -0.02107649 -0.08813749
203440_at  0.16638427  1.41150577  0.27423018

The process I perform is:

R> res <- gedBlood(tapas2)
Error in `rownames<-`(`*tmp*`, value = c("Th", "Th act", "Tc", "Tc act",  :
  attempt to set 'rownames' on an object with no dimensions
Timing stopped at: 0.084 0 0.084
Timing stopped at: 0.439 0 0.439

I checked the annotation of the abbas data-set:

R> abbas
ExpressionSet (storageMode: lockedEnvironment)
assayData: 359 features, 17 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: Th Th act ... neutro (17 total)
  varLabels: Name Type WBType Method
  varMetadata: labelDescription
featureData
  featureNames: 242904_x_at 232165_at ... 223809_at (359 total)
  fvarLabels: AFFY ENTREZID SYMBOL Name
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: hgu133a.db hgu133b.db

As far as I know, it should work since both are in hgu133b. So, what's happening on the gedBlood function to crash?

 

 

cellmix microarray deconvolution • 1.7k views
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