[BioC] Error from using featureFilter (genefilter package)

[ywchen at jimmy.harvard.edu]

Dear Wolfgang,

Thank you very much. I will try R 2.9 as well as with the public dataset,

Best,
Yiwen
Quoting Wolfgang Huber <huber at ebi.ac.uk>:

> 
> Dear Yiwen
> 
> thanks for the details. Unfortunately, you are using an older version of 
> R and Bioconductor. I noted that the rowQ function has changed recently, 
> and suggest you try with R 2.9 and the associated releases of all 
> packages (in particular Biobase and genefilter). Please understand that 
> it is not practical for us to support past, obsolete versions of the 
> software.
> 
> Can you please check whether you then still get that problem?
> 
> Also, for maximum effectiveness in getting help from others, consider 
> providing self-contained examples that use publicly visible datasets (I 
> do not have the CEL files in your home directory, hence cannot reproduce 
> your code example). There are example datasets, e.g., in the affydata 
> package. Or you can use the ArrayExpress package to download any of 
> thousands public datasets:
> http://www.bioconductor.org/packages/2.4/bioc/html/ArrayExpress.html
> 
> Best wishes
>       Wolfgang
> 
> ------------------------------------------------
> Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
> 
> ywchen at jimmy.harvard.edu ha scritto:
> > 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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> 
> 
> -- 
>