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

[Jia, Li (NIH/NCI) [C]]

Hi Jim,

Thanks for the prompt reply. When I tested on the first command you sent
to us, it generated an error.

> x <- varMetadata(pd)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘varMetadata’ for
signature ‘"data.frame"’



Please advise again. Thanks a lot.

Li

On 7/24/13 4:58 PM, "James W. MacDonald" <jmacdon at uw.edu> wrote:

>
>
>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
>>
>> --
>> 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
>