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

[James W. MacDonald]

You have to create the AnnotatedDataFrame first.

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

Best,

Jim


On 7/24/2013 5:03 PM, Jia, Li (NIH/NCI) [C] wrote:
> 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
>>>
>>> --
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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
>>

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