[BioC] Problems using text to subset array information from an expression set
land0038 at umn.edu
Tue Apr 4 20:15:42 CEST 2006
I have an odd problem that I cannot seem to figure out.
I have a set of CEL files in a directory, which I read using the ReadAffy()
command. Then I run the rma command to preprocess.
> Data <- ReadAffy()
> alldata <- rma(Data)
I've done this many times before without problems. However, when I try to
use text instead of numbers for subscripting, I get an error.
For example, I am able to access data from the first row and column using
Expression Set (exprSet) with
phenoData object with 1 variables and 1 cases
sample: arbitrary numbering
but using text for either subscript, I get an error.
Error in alldata["1007_s_at", ] : no 'dimnames' attribute for array
Error in alldata[, "AA100.CEL"] : no 'dimnames' attribute for array
I actually went through what I think was the same process last week (and
many times previously) and had no problems, so I'm stumped.
Here is my session information:
R version 2.1.0, 2005-04-18, ia64-unknown-linux-gnu
attached base packages:
 "tools" "methods" "stats" "graphics" "grDevices" "utils"
 "datasets" "base"
other attached packages:
hgu133acdf affy reposTools Biobase
"1.4.3" "1.6.7" "1.5.19" "1.5.12"
I must be missing something obvious, but I just can't figure out what is
going wrong. Does anyone have insight into this problem?
University of Minnesota
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