[BioC] merging columns of large data sets
mtmorgan at fhcrc.org
Sat Sep 26 22:11:32 CEST 2009
Amit Kumar wrote:
> Hi! All
> I am trying to merge very large data sets. Here fullset1 contains 13
> ExpressionSets. Each data set has columns containing Cy5 and Cy3
> intensities which I need to merge.
> Here I am trying to merge columns (containing Cy5 intensity)
> 2,6,10,14....till end for all 13
> data sets in fullset1. But I am only getting 2nd column from each of
> the 13 data sets.
> Rchan1 = sapply(1:length(fullset1), function(i) exprs(fullset1[[i]])[ ,2])
> Rch1 = as.list(Rchan1)
> red1 = do.call(cbind,Rch1)
looks like you want columns in
seq(2, ncol(exprs), 4)
so, assuming fullset1 is a list,
red1 = lapply(fullset1,
function(eset) exprs(est)[,seq(2, ncol(eset), 4)])
red = do.call(cbind, red1)
No need to cross-post (to the R and Bioc mailing lists)
> Likewise, here I need to merge columns (containing Cy3 intensity)
> 3,7,11,15...till end for all 13
> data sets in fullset1. And I am getting 3rd column from each of the 13
> data sets.
> Gchan1 = sapply(1:length(fullset1), function(i) exprs(fullset1[[i]])[ ,3])
> Gch1 = as.list(Gchan1)
> green1 = do.call(cbind,Gch1)
> I am stuck! Please Help! If its not possible this way please suggest
> me alternative way to do it.
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