[BioC] Oligo package error

[James W. MacDonald]

Try adding your AnnotatedDataFrame after creating the 
ExpressionFeatureSet:

dat <- read.celfiles(list.celfiles())
phenoData(dat) <- pd

Best,

Jim



On Friday, November 08, 2013 12:44:58 PM, guest [guest] wrote:
>
> Hi, I'm getting this error when I try to read in  my cel files. These are mouse ST 2.0 arrays
>
> Error:
>
> Error in validObject(out) : invalid class “GeneFeatureSet” object:
>    NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see
>      ?"channelNames<-,NChannelSet,character-method"
>
> 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.
>
> Thanks.
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> 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.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.
>
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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