[BioC] Problems using text to subset array information from an expression set
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Tue Apr 4 23:04:07 CEST 2006
Jeff: you are using a very old version of Biobase (1.5.12). If I use
a current version (1.8.0) I can subset exprSet's in the way you want
(tested by running the example for exprSet and then subsetting using
It might also (instead of just being an old version) be because of
the way the exprSet is constructed using rma. Could you do the following
1) Do a traceback() after the error
2) test what the rownames/colnames are of
I assume that se.exprs(Data) is a <0 x 0 matrix>.
On Apr 4, 2006, at 11:31 AM, Benilton Carvalho wrote:
> exprs(alldata)[, "AA100.CEL"]
> what you want?
> On Tue, 4 Apr 2006, Jeff Lande wrote:
>> 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
>> 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
>> 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.
>> 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"
>>  "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
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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