[BioC] subsetting an eset object with a defined list

Sean Davis sdavis2 at mail.nih.gov
Thu Oct 5 12:42:38 CEST 2006

On Thursday 05 October 2006 06:27, Celine Carret wrote:
> Hi,
> I'm stuck remembering the way of subsetting an eset object (19 affy
> arrays) to accomodate only a defined list of genes that I'm interested in.
> I read.table(list) into R, transformed it as.matrix and use the functions:
> exprs(eset)[list] or
> exprs(eset)[as.character(list)]
> those functions recognize that I have 904 genes in that list, but gives
> me 904 NA
> What I would like to obtain is my 904 genes with the values for the 19
> arrays, in order to assess the DE only on this subgroup as the other
> genes are not supposed to be expressed at this stage of the cultures I'm
> looking at.
> Could someone please point me in the right direction?

I think it might be best if you post the exact code that you used.  There are 
several statements that will likely give errors.  Can you send the input and 
(possibly abbreviated) output from R?


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