Question: Using affy package to process raw data (.cel files) from GEO: Going from GSExxx.tar to .cel
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gravatar for sbr0012
2.5 years ago by
sbr00120
sbr00120 wrote:

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!

R gene • 1.5k views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.5 years ago by sbr00120

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Santosh Anand5.0k
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