Dear group, I have 50 CEL files. I have the expression values and the colnames extracted as matrix files. The colnames are named with the .cel file names. Now in a different file the .CEL files are referenced to sample name. I am interested in classifying the studies based on samples. The other file looks like this: XXXXXXXXX.CEL xxKL_98 XXXXXxxxX.CEL X2KL_98 XXXXXXXXX.CEL X4KL_99 ..... Now in R my output looks like this: > colnames(gliexp)[1:6] [1] "XXXXXXXXX.CEL" "XXXXXXXXXXX.CEL" "XXXXXXXXXX.CEL" "XXXXXXXXXXXXXXXX.CEL" "XXXXXXXXXXX.CEL" I tried using grep function and it takes up only one pattern. If I have to do this for whole study I would have to do 150 times and I cannot do that. Is there some way similar to grep() or just grep() itself where it takes more patterns. where I can define certain files (as patterns) as one go and classiffy them as some category. The file names are unique with numbers and doe not seem to have specific pattern. Please help me. thank you Cheers S

mat <- matrix( rnorm(6), nc=3 ) colnames(mat) <- c( "C.cel", "A.cel", "B.cel" ) mat C.cel A.cel B.cel [1,] -0.7519613 -0.8182346 0.4788695 [2,] -1.7171199 1.4231551 0.5341957 mapping <- cbind( c("A.cel", "B.cel", "C.cel"), c("first", "second", "third") ) mapping [,1] [,2] [1,] "A.cel" "first" [2,] "B.cel" "second" [3,] "C.cel" "third" match( as.character(colnames(mat)), as.character(mapping[ ,1]) ) [1] 3 1 2 ord <- match( colnames(mat), as.character(mapping[ ,1]) ) colnames(mat) <- mapping[ ord, 2 ] mat third first second [1,] -0.7519613 -0.8182346 0.4788695 [2,] -1.7171199 1.4231551 0.5341957 On Fri, 2004-08-13 at 22:53, S Peri wrote: > Dear group, > > I have 50 CEL files. I have the expression values and > the colnames extracted as matrix files. The colnames > are named with the .cel file names. Now in a different > file the .CEL files are referenced to sample name. I > am interested in classifying the studies based on > samples. > The other file looks like this: > > XXXXXXXXX.CEL xxKL_98 > XXXXXxxxX.CEL X2KL_98 > XXXXXXXXX.CEL X4KL_99 > ..... > > > > Now in R my output looks like this: > > > colnames(gliexp)[1:6] > > [1] "XXXXXXXXX.CEL" "XXXXXXXXXXX.CEL" "XXXXXXXXXX.CEL" > "XXXXXXXXXXXXXXXX.CEL" "XXXXXXXXXXX.CEL" > > > I tried using grep function and it takes up only one > pattern. If I have to do this for whole study I would > have to do 150 times and I cannot do that. > Is there some way similar to grep() or just grep() > itself where it takes more patterns. where I can > define certain files (as patterns) as one go and > classiffy them as some category. The file names are > unique with numbers and doe not seem to have specific > pattern. > > Please help me. > thank you > > Cheers > S > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >