[BioC] Extracting expressions after a multtest procedure (part 2)

Sean Davis sdavis2 at mail.nih.gov
Sun Mar 16 17:38:11 CET 2008

On Sun, Mar 16, 2008 at 11:56 AM, JUAN MIGUEL MARIN DIAZARAQUE
<jmmarin at est-econ.uc3m.es> wrote:
> Hello,
>  In previous message I wonder how to extract just the expressions of 102
>  genes under two conditions after a multtest procedure.
>  At last, I wrote this unelegant code that seems to work:
>  quedan <- resT[res$adjp[,"BH"]<0.05,]
>  busco <- dimnames(quedan)[[1]]
>  cosa <- NULL
>  for (i in 1:length(dimnames(exprs(esetSub))[[1]]))
>         for (j in 1:length(busco))
>                 if (dimnames(exprs(esetSub[i,]))[[1]] == busco[j]) {
>                 cosa <- rbind(cosa, as.data.frame(exprs(esetSub))[i,]) }
>         end
>  end

Generally, you can subset ExpressionSets just like you do data frames;
rows are genes or probes and columns are samples.  If esetSub is what
you used for your multtest procedure, you should be able to do:


In general, for loops are quite useful in R, but for things like
subsetting or vectorized operations, it is better to look for other
alternatives as they are likely to be faster.


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