[BioC] Input regarding sorting out candidate genes from edgeR results

Sindre Lee sindre.lee at studmed.uio.no
Mon Mar 10 19:07:47 CET 2014

I have been asked to make a candidate list of genes for downstream 
analysis. We are going to look for secreted proteins into plasma from 
muscle tissue. I started by picking out genes coding for secretory 
Then I sorted by fold change and prediction score, but then I started 
wondering what actually gives a huge fold change, and now Im not so sure 
if this is the best approach? Do anyone here have experience with this 
and have some good ideas? Maybe run GSEA, cluster genes with same 
expression profile etc?

The reason I ask is to try and save money spent on ELISA kits.

Thank you very much!

Best regards,

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