On Thursday 01 March 2007 06:48, Daniel Brewer wrote: > Sean Davis wrote: > > On Thursday 01 March 2007 05:31, Daniel Brewer wrote: > >> What is the best way to import (what I believe is) a Affymetrix GCOS > >> produced tab-delimited results file for use with limma and the like? > >> > >> Unfortunately I do not have access to the CEL files. > > > > I'm not sure what format the files are, but you might want to look at > > read.maimages() in the limma package. Alternatively, you can use > > read.table for each array and then put the columns together any way you > > like using R commands. There might be better ways, besides the two > > mentioned here. > > > > Sean > > Thanks. > > Just for completeness, here is the first couple of lines of one of the > files: > Descriptions Met 1_Signal Met 1_Detection Met 1_Detection p-value Met > 2_Signal Met 2_Detection Met 2_Detection p-value Met 3_Signal Met > 3_Detection Met 3_Detection p-value Met 4_Signal Met 4_Detection Met > 4_Detection p-value Met 5_Signal Met 5_Detection Met 5_Detection > p-value Met 6_Signal Met 6_Detection Met 6_Detection p-value Met > 7_Signal Met 7_Detection Met 7_Detection p-value Met 8_Signal Met > 8_Detection Met 8_Detection p-value > AFFX-BioB-5_at "J04423 E coli bioB gene biotin synthetase (-5, -M, -3 > represent transcript regions 5 prime, Middle, and 3 prime > respectively)" 624.4 P 0.002275 955.7 P 0.000857 629.5 P 0.002275 > 819.4 P 0.000972 456.4 P 0.001593 498 P 0.002275 470.7 P 0.002275 > 1141.6 P 0.000509 So, just read this with read.table(). Then, you can get various matrices like so: dat <- read.table(....) signalMatrix <- as.matrix(dat[,seq(2,ncol(dat),3)]) # extract every third column starting with the second column detectionMatrix <- as.matrix(dat[,seq(3,ncol(dat),3]) # And start with the third column, etc. .... You can use these matrices to make whatever data structure you like, or just use the matrix directly with limma. Sean