[BioC] oligo package reading in cel files

[James W. MacDonald]

Does

exp.data <- read.celfiles(list.celfiles(), phenodata=pd)

work?

Otherwise, please give the output from

celfiles

and

traceback()

after the error.

Best,

Jim



On Monday, October 28, 2013 2:50:10 PM, oligo user [guest] wrote:
>
> Hi I'm trying to read in cel file names from Affy MoGene-2_0-st arrays, however I am receiving error message indicating that my cel file names are not of the character class when it appears that they are. My phenodata is read in successfully.
>
> Here is my code and error:
>
>
>> celfiles = list.files(path = ".", pattern = ".CEL$", all.files = FALSE,
> full.names = FALSE, recursive = FALSE, ignore.case = FALSE);
>
>> pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Filename" ,sep="\t")
>
>> exp.data = read.celfiles(filenames=celfiles,phenodata=pd)
> Error: is.character(filenames) is not TRUE
>
>> class(celfiles)
> [1] "character"
>
>> is.character(celfiles)
> [1] TRUE
>
>
> Any advice will be appreciated.
>
> Thanks!
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> 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] affyPLM_1.36.0             preprocessCore_1.22.0      arrayQualityMetrics_3.16.0
>   [4] affyQCReport_1.38.0        lattice_0.20-15            simpleaffy_2.36.1
>   [7] gcrma_2.32.0               genefilter_1.42.0          affy_1.38.1
> [10] pd.mogene.2.0.st_2.12.0    RSQLite_0.11.4             DBI_0.2-7
> [13] oligo_1.24.2               Biobase_2.20.1             oligoClasses_1.22.0
> [16] BiocGenerics_0.6.0         BiocInstaller_1.10.4
>
> 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_1.2-4
> [13] ff_2.2-12            foreach_1.4.1        GenomicRanges_1.12.5 grid_3.0.1
> [17] Hmisc_3.12-2         hwriter_1.3          IRanges_1.18.4       iterators_1.0.6
> [21] latticeExtra_0.6-26  limma_3.16.8         plyr_1.8             RColorBrewer_1.0-5
> [25] reshape2_1.2.2       rpart_4.1-1          setRNG_2011.11-2     splines_3.0.1
> [29] stats4_3.0.1         stringr_0.6.2        survival_2.37-4      SVGAnnotation_0.93-1
> [33] tools_3.0.1          vsn_3.28.0           XML_3.95-0.2         xtable_1.7-1
> [37] 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