[BioC] Error from using featureFilter (genefilter package)
Martin Morgan
mtmorgan at fhcrc.org
Sun May 17 23:15:41 CEST 2009
Hi Yiwen,
The error
>> > Error in rowQ(exprs(imat), which) :
>> > which is larger than the number of rows
comes about when rowQ tries to calculate an order statistic that
doesn't make sense, e.g., the 0th quantile of a matrix with 0 columns
> rowQ(matrix(0, nrow=10, ncol=0), 0)
Error in rowQ(matrix(0, 0, 0), 0) :
which is larger than the number of rows
(the error message in the release version is more correct when it says
'cannot calculate order statistic on object with 0 columns') so my
guess is your criteria have eliminated all your probe sets. You could
verify this with
debug(featureFilter)
and then evaluating your featureFilter() command, and stepping through
(see ?browser) the function. undebug(featureFilter) when done.
Martin
<ywchen at jimmy.harvard.edu> writes:
> 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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>>
>>
>> --
>>
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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