[BioC] Problems using text to subset array information from an expression set

Jeff Lande 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
numeric subscripts

> alldata[1,1]
Expression Set (exprSet) with
        1 genes
        1 samples
                 phenoData object with 1 variables and 1 cases
                sample: arbitrary numbering

but using text for either subscript, I get an error.

> alldata["1007_s_at",]
Error in alldata["1007_s_at", ] : no 'dimnames' attribute for array
> alldata[,"AA100.CEL"]
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:

> sessionInfo()
R version 2.1.0, 2005-04-18, ia64-unknown-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "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?

Jeff Lande
Post-Doctoral Associate
University of Minnesota

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