[BioC] rowQ error

Dennis.Burian at faa.gov Dennis.Burian at faa.gov
Thu Jan 31 22:29:50 CET 2008

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)


   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
   > CHT_veset
   ExpressionSet (storageMode: lockedEnvironment)
   assayData: 54675 features, 29 samples
     element names: exprs
     sampleNames: T1_S13.CEL, T1_S15.CEL, ..., T5_S8.CEL  (29 total)
     varLabels and varMetadata description:
       sample: arbitrary numbering
     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))
   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
dennis.burian at faa.gov

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