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) 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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793