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

[Benilton Carvalho]

isn't

  exprs(alldata)["1007_s_at",]
  exprs(alldata)[, "AA100.CEL"]

what you want?

b

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 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
>         varLabels
>                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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