[BioC] oligo package attaching phenodata for HuGene2.0 ST array

[Guest [guest]]

Hi,

We are working with affymetrix HuGene2.0 ST arrays and are trying to read in our CEL files with the oligo package. However, we are having trouble integrating our phenodata to the expression data. Please see our code and error message below. The covdesc.txt is the file with our phenodata.

code:

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

OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd, verbose = TRUE)

>pData(pd)
        Filename Treatment Transfection
1      ACsiNS.CEL   control     ns_siRNA
2     ACSsi03.CEL   control      siRNA03
3    ANCSsi03.CEL   Treated      siRNA03
4  ANCSsiNS_2.CEL   Treated     ns_siRNA
5      DCsi03.CEL   control     ns_siRNA
6      DCsiNS.CEL   control      siRNA03
7    DNCSsi03.CEL   Treated      siRNA03
8    DNCSsiNS.CEL   Treated     ns_siRNA
9      ECsi03.CEL   control     ns_siRNA
10     ECsiNS.CEL   control      siRNA03
11   ENCSsi03.CEL   Treated      siRNA03
12   ENCSsiNS.CEL   Treated     ns_siRNA

Error:
> OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd1, verbose = TRUE)
Platform design info loaded.
Reading in : ACsiNS.CEL
Reading in : ACSsi03.CEL
Reading in : ANCSsi03.CEL
Reading in : ANCSsiNS_2.CEL
Reading in : DCsi03.CEL
Reading in : DCsiNS.CEL
Reading in : DNCSsi03.CEL
Reading in : DNCSsiNS.CEL
Reading in : ECsi03.CEL
Reading in : ECsiNS.CEL
Reading in : ENCSsi03.CEL
Reading in : ENCSsiNS.CEL
Error in validObject(out) : invalid class “GeneFeatureSet” object: 
  'NChannelSet' varMetadata must have a 'channel' column

Any suggestions will be appreciated!
Thanks!


 -- output of sessionInfo(): 

> sessionInfo() 
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[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.hugene.2.0.st_3.8.0     RSQLite_0.11.4             DBI_0.2-7                 
 [4] oligo_1.24.1               oligoClasses_1.22.0        affyPLM_1.36.0            
 [7] preprocessCore_1.22.0      arrayQualityMetrics_3.16.0 affyQCReport_1.38.0       
[10] lattice_0.20-15            simpleaffy_2.36.1          gcrma_2.32.0              
[13] genefilter_1.42.0          affy_1.38.1                Biobase_2.20.1            
[16] BiocGenerics_0.6.0         BiocInstaller_1.10.2      

loaded via a namespace (and not attached):
 [1] affxparser_1.32.3    affyio_1.28.0        annotate_1.38.0      AnnotationDbi_1.22.6
 [5] beadarray_2.10.0     BeadDataPackR_1.12.0 Biostrings_2.28.0    bit_1.1-10          
 [9] Cairo_1.5-2          cluster_1.14.4       codetools_0.2-8      colorspace_1.2-2    
[13] ff_2.2-11            foreach_1.4.1        GenomicRanges_1.12.4 grid_3.0.0          
[17] Hmisc_3.12-2         hwriter_1.3          IRanges_1.18.2       iterators_1.0.6     
[21] KernSmooth_2.23-10   latticeExtra_0.6-24  limma_3.16.6         plyr_1.8            
[25] RColorBrewer_1.0-5   reshape2_1.2.2       rpart_4.1-1          setRNG_2011.11-2    
[29] splines_3.0.0        stats4_3.0.0         stringr_0.6.2        survival_2.37-4     
[33] SVGAnnotation_0.93-1 tools_3.0.0          vsn_3.28.0           XML_3.95-0.2        
[37] xtable_1.7-1         zlibbioc_1.6.0      

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