how to perform cross platform gene expression analysis

Question

[nazaninhoseinkhan]

Hi all,

I am trying to find differential expressed genes(DEG) among different platforms(cross platform).

I know that at first the shared genes among different platforms must be detected. But I don't know how to do that.

Can anybody give me a clue how to perform the above task?

Thank u in advance

Nazanin

Answer 1

[Devon Ryan]

Generally people would use Combat from the SVA package to try and correct for the inter-platform batch effect and then use the corrected values for the DE analysis.