[BioC] problem with justRMA in 2.10.0

[James W. MacDonald]

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