Greetings, R version 2.7.0 (2008-04-22) i386-pc-mingw32 I am retrieving the probe indexes using the indexProbes function for each of the gene names. nbatch <- normalize.AffyBatch.quantiles(abatch,type="pmonly") gn <- geneNames(nbatch) gene_indexes <- indexProbes(nbatch, which="pm", genenames=gn) I found that I need to cast the indexes as.character to retrieve the normalized pm values. log2(pm(nbatch)[as.character(gene_indexes[[i]]),]) Actually I am using an lapply function: LG <- function(x, ma) { return(log2(ma[as.character(x),])) } LIGC <- lapply(Rpm , LG, ma=pm(nbatch)) This worked until I ran into an error at index=100000 because it was converted to "1e+05" and log2(pm(nbatch)[as.character(gene_indexes[[374]]),]) Error: subscript out of bounds > as.character(gene_indexes[[374]]) [1] "24439" "3897" "1e+05" "29082" "53595" "53100" "65653" "13262" [9] "45563" "29747" "29735" "105476" "46438" "83596" "23127" "36490" [17] "105458" "16956" "98869" "74954" "23587" Can someone suggest something get me thru this problem? Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu

Greetings again, I was able to fix my last message by using options(scipen). However, this call coversion to character is too time consuming. pm(nbatch)[as.character(gene_indexes[[i]]),] Is there a better way to retrieve the "pm" probe normalized expression values clustered by gene? Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu