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?