[BioC] oligo package reading in cel files

oligo user [guest] guest at bioconductor.org
Mon Oct 28 19:50:10 CET 2013

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. 


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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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