Meta Analysis of Data from GEO

Question

[smectutor]

HI everyone,

I'm trying to use data from GEO in a meta-analysis study. Im using a wide variety of datasets some from mice and humans microarray studies. I found the software A-madman promising however, the software is riddled with errors if GEO data doesn't conform to some standard.or there is missing information in the GEO files.

Does anyone have any other freeware software that could help me?

Answer 1

[Chris Evelo]

If I understand you correctly you try to use lots of data from GEO and your software thinks that some of it is not good enough. You should be careful about cheating your software in thinking differently since it might actually be right. Not all data in repositories is as good as it should be.

If you are not looking for specific sets that really need to be fixed I would suggest an alternative approach. For the European counterpart of GEO, ArrayExpress: (https://www.ebi.ac.uk/arrayexpress/ ), there is a curated and quality controlled and in part standard treated subset available at Expression Atlas (https://www.ebi.ac.uk/gxa/home). This might serve your purposes better.