[BioC] Error from using featureFilter (genefilter package)

[Wolfgang Huber]

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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