Removing batch effects between Affymetrix and Agilent platforms using ComBat

Question

[nazaninhoseinkhan]

Dear all,

I want to integrate microarray data from different platforms (Affymetrix and Agilent).

I know that ComBat function which is now is a part of SVA package can be used for reving batch effects from microarray data.

Can I use ComBat function for integrating these data? and if yes, does it make difference which strategy I use for obtaining the list of deregulated genes?

Thank u in advance for your advice

Nazanin

Answer 1

[andrew.j.skelton73]

I suggest you have a look at my answer here, which may clarify some batch correction limitations.