[BioC] problem with justRMA in 2.10.0
James W. MacDonald
jmacdon at med.umich.edu
Wed Nov 4 16:23:12 CET 2009
Hi Fraser,
Thanks for the bug report. Fixed in devel and released versions now, and
should propagate for download within a day or so.
Best,
Jim
Fraser Sim wrote:
> I'm getting a cryptic error message when trying to run justRMA on a folder
> of files, with the file names specified in celFiles. I am not setting the
> phenoData or protocolData at this point and just want the eset populated
> with the default pData. This code worked fine under 2.9.2. Thanks, Fraser
>
> Here's my code:
>
>> library(affy)
>> eset <- justRMA(filenames = celFiles)
> Error in validObject(.Object) :
> invalid class "AffyBatch" object: 1: sample numbers differ between
> phenoData and protocolData
> invalid class "AffyBatch" object: 2: sampleNames differ between phenoData
> and protocolData
>> all(celFiles %in% list.files())
> [1] TRUE
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] affy_1.24.0 Biobase_2.6.0 rcom_2.2-1 rscproxy_1.3-1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.0
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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