Writing Background correction code for a large number of CEL files

# This is the working back ground correction script
# Author: Sucheta
# Date: 9th Dec 2006

library(affy)

library(gcrma)

# Affinity info need not be calculated all the time, since it is
#mostly preserved with the workspace
#affinfo <- compute.affinities("soybean")


celfile<-read.table("list.txt") # read the elements of list.txt as a list

celfile<-as.matrix(celfile) # convert celfile from a list to a matrix

n<-dim(celfile)[1] # Getting the number of cel files

m <- 18;

dir<-"/home/XXX/cel/"

outdir<-"/home/XXX/bgCorrect/"




print(n);


k <- (m - 2*m)+1;

i<- k;

while( { i = i + m } < n){ # Replace for loop with while loop

print(i);

file <- NULL;
obj <- NULL;
tmp1 <- NULL;

for(j in 0:(m-1)){

tmpFile <- paste(dir, celfile[i+j], sep="");

file <- c(file, list(tmpFile)) # appending a list to the existing list

}

obj<-ReadAffy(filenames=file)


tmp1<-bg.adjust.gcrma(obj,optical.correct=T,affinity.info=affinfo)

outfile<-paste(outdir, celfile[i,1], "_bg.txt", sep="")

write.table(pm(tmp1), file=outfile, row.names=FALSE, col.names=TRUE, sep="\t")


}