How to convert GMS file into expression file

Question

[cmrcln]

Hi all,

I am trying to get the processed data for GSE58679. According to information given by authors of the paper, processed data as well as the raw data should be available. However, I am not able to find the processed data in this page. I have checked all SOFT, Miniml, and series matrix file by unzipping and opening them in excel. They contain nothing but metadata. I have tried GeoQuery package to convert GSE file to Expression levels, however my knowledge on R is limited, so couldn't figure out how to get expression value. I do not even need all the samples, but just GSM1416802 and GSM1416803 will suffice. GEO2R is not available for these samples. I would greatly appreciate any help.

Thanks,

Answer 1

[Devon Ryan]

One of the gzipped txt files appears to contain counts for 42 or so genes for all of the samples. Perhaps that's useful for you. In general, RNAseq experiments don't get uploaded with much processed data. Don't expect the soft or series matrix files to ever have values for them. If you just want a couple samples, then download and align them. That's a pretty quick process.