[BioC] merging columns of large data sets

[Martin Morgan]

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)

Martin

> 
> 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.
> 
> Cheers!
> Amit
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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