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

[James W. MacDonald]

On 7/24/2013 4:40 PM, Guest [guest] wrote:
> 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!

There is a varMetadata slot to the AnnotatedDataFrame, and oligo expects 
that there will be a column called 'channel'. A really cheap way to fix 
this would be to do something like

x <- varMetadata(pd)
x <- data.frame(x, channel = "_ALL_")
varMetadata(pd) <- x

and then proceed with read.celfiles().

Best,

Jim


> 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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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099