[BioC] Error from using featureFilter (genefilter package)

[ywchen at jimmy.harvard.edu]

Hi Robert,

Thanks for the information. The following is an example along with the
sessionInfo().

Best,
Yiwen


library(affy)
library(genefilter)
data<-ReadAffy()
eset<-rma(data)
non_ed<-nsFilter(eset,require.entrez=TRUE,require.GOBP=TRUE,remove.dupEntrez=TRUE,feature.exclude="^AFFX")

non_ed$filter.log
$numLowVar
[1] 6513

$numDupsRemoved
[1] 15899

$feature.exclude
[1] 10

$numNoGO.BP
[1] 12996

$numRemoved.ENTREZID
[1] 12745

ed<-featureFilter(eset,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
traceback()
8: .Call("rowQ", imat, which, PACKAGE = "Biobase")
7: rowQ(exprs(imat), which)
6: rowQ(exprs(imat), which)
5: rowQ(eSet, floor(0.25 * numSamp))
4: rowQ(eSet, floor(0.25 * numSamp))
3: rowIQRs(eset)
2: findLargest(featureNames(eset), rowIQRs(eset), annotation(eset))
1: featureFilter(eset, require.entrez = TRUE, require.GOBP = TRUE, 
       remove.dupEntrez = TRUE, feature.exclude = "^AFFX")

sessionInfo()
R version 2.8.1 (2008-12-22) 
i386-apple-darwin8.11.1 

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
methods   base     

other attached packages:
[1] hgu133plus2.db_2.2.5 RSQLite_0.7-1        DBI_0.2-4           
AnnotationDbi_1.4.3  hgu133plus2cdf_2.3.0 genefilter_1.22.0    survival_2.34-1 
    affy_1.20.2          Biobase_2.2.2       

loaded via a namespace (and not attached):
[1] affyio_1.10.1        annotate_1.20.1      preprocessCore_1.4.0




> 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
>     Robert
> 
> > "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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> > Bioconductor at stat.math.ethz.ch
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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
> 206-667-7700
> rgentlem at fhcrc.org
>