[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)
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))
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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