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!