Using affy package to process raw data (.cel files) from GEO: Going from GSExxx.tar to .cel

Question

[sbr0012]

Hi,

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) [1] 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?

Thanks!

[Santosh Anand]

Please format your code using code-formatting button (10101010). It's illegible currently!

Answer 1

[yve_yt]

Just rename your "gsmxxxxxx.cel.gz" files to remove the .gz extension, and you're good to go with readaffy