blood deconvolution - cellmix
0
1
Entering edit mode
9.2 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?

microarray deconvolution cellmix • 2.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 1570 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6