[BioC] Error from using featureFilter (genefilter package)

Robert Gentleman rgentlem at fhcrc.org
Fri May 15 19:44:30 CEST 2009

Hi Yiwen,

ywchen at jimmy.harvard.edu wrote:
> Dear all,
> I am a new user of Bioconductor. I was trying to use the function

  Well then, welcome.  You will need to spend a few minutes reading the posting
guide. Please make sure that you
   1) provide the output of sessionInfo() so we can figure out what version of
the software you are using
   2) provide a reproducible example so we can try it on our systems and
replicate the problem.

  best wishes

> "featureFilter" from genefilter package and got the following error message.
> nnon_ed<-featureFilter(ed,require.entrez=TRUE,require.GOBP=TRUE,remove.dupEntrez=TRUE,feature.exclude="^AFFX")
> Error in rowQ(exprs(imat), which) : 
>   which  is larger than the number of rows
> For the same dataset and parameters, I had no problem of using nsFilter
> function. I was wondering what is the possible reason for the error.
> Thank you very much.
> Sincerely,
> Yiwen Chen
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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