Download Raw Data From Geo As .Txt

Question

[ellenmseb]

Processed/normalized data from GEO is available easily as SOFT, MINiML, or .txt downloads, or through GEOquery.

But as far as I can tell, GEO provides raw data only as a .tar file (GSEXXXXX_RAW.tar) containing many .xls files.

Obviously I don't want to have to manually open up all (~200) of those xls files and save them as .txt for analysis. Has anyone found a better way to download raw data from GEO?

[Charles Warden]

I think your question requires knowledge about a specific platform.

For example, the GSEXXXXX_RAW.tar file for Affy data typically contains .CEL files. Tools for analyzing such Affy data typically use some sort of file list and not a conversion to .txt files (which is not trivial to begin with). I don't recall any platform that uses .xls files as the raw format (which is why it is hard for me to answer).

[Neilfws]

Yes, would be useful to point to a specific example GSE. It may be that raw just means "whatever submitter decides to provide", which may be xls in some cases, not others.

Answer 1

[January]

If you are using R, you can directly load the data with the package GEOquery:

library(GEOquery)
geo <- getGEO("GSE36238")

Until now, that was for me the ultimate way of getting data from GEO, since I usually process microarray data with R.

Apart from this, if the XLS files have a common structure, they can also be read and processed in a serial manner from R.