I'm trying to use the R package affy to pre-process and normalize raw microarray data I've downloaded from GEO. The data comes as a GSEXXX file containing a .txt file with sample information and gsexxs.tar file. This is what I've used so far:
library(GEOquery) getGEOSuppFiles("GSE16438") untar("GSE16438/GSE16438_RAW.tar", exdir="data") cels <- list.files("data/", pattern = "[gz]") length(cels)  24 sapply(paste("data", cels, sep="/"), gunzip) cels
So there are 24 samples in the raw data. I end up with 24 gsmxxxxxx.cel.gz files. I'm just not sure how I can use this information in affy. Do I have to unzip the files?