[BioC] Oligo package error

guest [guest] guest at bioconductor.org
Fri Nov 8 18:44:58 CET 2013

Hi, I'm getting this error when I try to read in  my cel files. These are mouse ST 2.0 arrays


Error in validObject(out) : invalid class “GeneFeatureSet” object: 
  NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see

Here is my code:

pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Filename" ,sep="\t")

celFiles <- list.celfiles()
x <- varMetadata(pd)
x <- data.frame(x, channel = "_ALL_")
varMetadata(pd) <- x
OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, verbose=T)

Any suggestions will be appreciated.


 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pd.mogene.2.0.st_2.12.0 RSQLite_0.11.4          DBI_0.2-7               oligo_1.26.0            Biobase_2.22.0         
[6] oligoClasses_1.24.0     BiocGenerics_0.8.0      BiocInstaller_1.12.0   

loaded via a namespace (and not attached):
 [1] affxparser_1.34.0     affyio_1.30.0         Biostrings_2.30.0     bit_1.1-10            codetools_0.2-8      
 [6] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.14.3  IRanges_1.20.5        iterators_1.0.6      
[11] preprocessCore_1.24.0 splines_3.0.2         stats4_3.0.2          tools_3.0.2           XVector_0.2.0        
[16] zlibbioc_1.8.0       

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list