Question: Converting GSE and GSM files from GEO to Eset
gravatar for maria.kesa
6.3 years ago by
maria.kesa30 wrote:


My goal is to obtain normalized gene expression values for this experiment on GEO. In order to achieve this goal, I understand that I have to first convert the files from GEO into expression set (eset) objects in R. And then I was planning to use justRMA. Would this be the correct way of doing things?

I was following this tutorial and it is quite easy to turn a GDS file from GEO into an eset, but I can't figure out how to do this for the GSE and GSM files for the concrete experiment that I need available on the GEO website. 

By the way, I have the GEOquery library installed and working.

Any help would be greatly appreciated!


eset geoquery R gene expression • 6.7k views
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by maria.kesa30
gravatar for Neilfws
6.3 years ago by
Sydney, Australia
Neilfws49k wrote:

The GEOquery vignette (PDF) explains how to work with GSE series matrix files.

ADD COMMENTlink written 6.3 years ago by Neilfws49k

Thank you so much, I was looking at that file, but somehow didn't see it (it's late here in Estonia:-)). I think I got it now. 

Do you know if it is appropriate to normalize the resulting expression ExpressionSet it using justRMA?

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by maria.kesa30

You'd have to check if the data are normalised already, by looking at the annotation of the sample files.

You may also want to look at the GEO2R link for that GSE, which allows simple analysis using R/limma online. However, that looks like a complex series with multiple platforms, so you could be in for some fun :)

ADD REPLYlink written 6.3 years ago by Neilfws49k

I have seen that most of the series matrix file for the microarray datasets are normalized intensity values but not log transformed. Atleast in the submitting guidelines it says so that the data should be normalized, but is there any way to know it is normalized or not from the series matrix files? I checked the GEO2R and checked at the distribution of the samples and also the annotation file. But no where it was that the data is normalized.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by ivivek_ngs5.0k

The link is broken, Can you update the link and explain how one can convert a GSE into an eset. Many Thanks

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by IsmailM110

I could, but I think you should be able to find the latest version quite easily by searching the Bioconductor website; the broken link takes you there. So that's an "exercise for the reader" :)

ADD REPLYlink written 4.0 years ago by Neilfws49k
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