[BioC] Error from using featureFilter (genefilter package)
ywchen at jimmy.harvard.edu
ywchen at jimmy.harvard.edu
Fri May 15 20:32:55 CEST 2009
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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> --
> 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
>
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