Hi Jim,

Thank you for the quick response.

exp.data <- read.celfiles(list.celfiles(), phenodata=pd) also does not work:


> exp.data = read.celfiles(filenames=list.celfiles(),phenodata=pd)

Error: is.character(filenames) is not TRUE


Output of celfiles:


> celfiles

 [1] "A1_(MoGene-2_0-st).CEL" "A2_(MoGene-2_0-st).CEL"
"A3_(MoGene-2_0-st).CEL"

 [4] "A4_(MoGene-2_0-st).CEL" "A5_(MoGene-2_0-st).CEL"
"B1_(MoGene-2_0-st).CEL"

 [7] "B2_(MoGene-2_0-st).CEL" "B3_(MoGene-2_0-st).CEL"
"B4_(MoGene-2_0-st).CEL"

[10] "B5_(MoGene-2_0-st).CEL" "C1_(MoGene-2_0-st).CEL"
"C2_(MoGene-2_0-st).CEL"

[13] "C3_(MoGene-2_0-st).CEL" "C4_(MoGene-2_0-st).CEL"
"C5_(MoGene-2_0-st).CEL"

[16] "D1_(MoGene-2_0-st).CEL" "D2_(MoGene-2_0-st).CEL"
"D3_(MoGene-2_0-st).CEL"

[19] "D4_(MoGene-2_0-st).CEL" "D5_(MoGene-2_0-st).CEL"
"E1_(MoGene-2_0-st).CEL"

[22] "E2_(MoGene-2_0-st).CEL" "E3_(MoGene-2_0-st).CEL"
"E4_(MoGene-2_0-st).CEL"

[25] "E5_(MoGene-2_0-st).CEL" "F1_(MoGene-2_0-st).CEL"
"F2_(MoGene-2_0-st).CEL"

[28] "F3_(MoGene-2_0-st).CEL" "F4_(MoGene-2_0-st).CEL"
"F5_(MoGene-2_0-st).CEL"

[31] "G1_(MoGene-2_0-st).CEL" "G2_(MoGene-2_0-st).CEL"
"G3_(MoGene-2_0-st).CEL"

[34] "G4_(MoGene-2_0-st).CEL" "G5_(MoGene-2_0-st).CEL"
"H1_(MoGene-2_0-st).CEL"

[37] "H2_(MoGene-2_0-st).CEL" "H3_(MoGene-2_0-st).CEL"
"H4_(MoGene-2_0-st).CEL"

[40] "H5_(MoGene-2_0-st).CEL" "I1_(MoGene-2_0-st).CEL"
"I2_(MoGene-2_0-st).CEL"

[43] "I3_(MoGene-2_0-st).CEL" "I4_(MoGene-2_0-st).CEL"
"I5_(MoGene-2_0-st).CEL"


Output from traceback after error:


> traceback()

4: stop(sprintf(ngettext(length(r), "%s is not TRUE", "%s are not all
TRUE"),

       ch), call. = FALSE, domain = NA)

3: stopifnot(is.character(filenames))

2: checkValidFilenames(filenames)

1: read.celfiles(filenames = list.celfiles(), phenodata = pd)

>


I appreciate your help!



On Mon, Oct 28, 2013 at 3:00 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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<http://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
>>
>>>
>>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>> ______________________________**_________________
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>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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