[BioC] rowQ error

[Robert Gentleman]

Hi Dennis,

Dennis.Burian at faa.gov wrote:
> I am using rowQ to filter on interquartile range on HgU133 plus2 Affy
> chips.  The following is my setup and a description of the ExpressionSet,
> and at the end, the error I'm getting "which  is larger than the number of
> rows" which is, of course, not true since both 13669 and 41006 are less
> than 54675, the number of rows in the ExpressionSet.
> 
>    > sessionInfo()
>    R version 2.6.0 (2007-10-03)
>    x86_64-unknown-linux-gnu
> 
>    locale:
>    LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
>    attached base packages:
>    [1] tools     stats     graphics  grDevices utils     datasets  methods
>    [8] base
> 
>    other attached packages:
>     [1] vsn_3.2.1            limma_2.12.0         geneplotter_1.16.0
>     [4] lattice_0.17-4       annotate_1.16.1      xtable_1.5-2
>     [7] AnnotationDbi_1.0.6  RSQLite_0.6-4        DBI_0.2-4
>    [10] hgu133plus2cdf_2.0.0 affy_1.16.0          preprocessCore_1.0.0
>    [13] affyio_1.6.1         Biobase_1.16.1
> 
>    loaded via a namespace (and not attached):
>    [1] grid_2.6.0         KernSmooth_2.22-21 RColorBrewer_1.0-2
>    rcompgen_0.1-17
>    > CHT_veset
>    ExpressionSet (storageMode: lockedEnvironment)
>    assayData: 54675 features, 29 samples
>      element names: exprs
>    phenoData
>      sampleNames: T1_S13.CEL, T1_S15.CEL, ..., T5_S8.CEL  (29 total)
>      varLabels and varMetadata description:
>        sample: arbitrary numbering
>    featureData
>      featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at  (54675 total)
>      fvarLabels and fvarMetadata description: none
>    experimentData: use 'experimentData(object)'
>    Annotation: hgu133plus2
>    > lowQ<-rowQ(exprs(CHT_veset), floor(13669))


   rowQ is computing the quantiles for the row, so you only have 29 
observations.  The error is trying to tell you that.

   If you want to filter so that you choose the 13669 rows with the 
largest IQRs (or something like that) you should use the nsFilter 
function. nsFilter also takes care of duplicate EntrezGene IDs (if you 
want it to).

  (and as an aside, you can just do:  lowQ<-rowQ(CHT_veset, 13)
   or lowQ<-rowQ(CHT_vest, 13L) if you are really wanting to be careful)


  hope that helps
    Robert

>    Error in rowQ(exprs(CHT_veset), floor(13669)) :
>      which  is larger than the number of rows
>    > upQ<-rowQ(CHT_veset, ceiling(41006))
>    Error in rowQ(exprs(imat), which) :
>      which  is larger than the number of rows
> 
> Dennis Burian, Ph.D.
> Functional Genomics Group
> Civil Aerospace Medical Institute, AAM-610
> 6500 S. MacArthur Blvd.
> Oklahoma City OK  73169
> 405-954-6087
> dennis.burian at faa.gov
> 
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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, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org