Question: Download Raw Data From Geo As .Txt
gravatar for ellenmseb
5.5 years ago by
ellenmseb0 wrote:

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?

ADD COMMENTlink modified 5.5 years ago by January30 • written 5.5 years ago by ellenmseb0

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).

ADD REPLYlink written 5.5 years ago by Charles Warden7.2k

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.

ADD REPLYlink written 5.5 years ago by Neilfws48k
gravatar for January
5.5 years ago by
January30 wrote:

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.

ADD COMMENTlink written 5.5 years ago by January30
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