GSEA and IPA: alternative or complementary?

Question

[Mozart]

Dear all, I have read a couple of papers where people used both GSEA and IPA for their analysis in their pipeline and tried to justify this approach by saying that they tried to confirm results found in IPA with GSEA too. What do you think? Does it make any sense to you?

regards,

[GenoMax]

Qiagen has a product called Omicsoft (and various sub types like Omicsoft OncoLand) that would be more of an equivalent of what GSEA provides in terms of other published datasets that are similar to your samples. It requires a separate license so it may not be available in your case.

[Mozart]

Thanks a lot for this clarification. I will try to look at the Omicsoft deeper if I can. But what if one has to draw conclusions for like 'defending' the idea according to which both tools are used (I mean, IPA and GSEA)?

Answer 1

[igor]

Broadly speaking, pathway analysis is meant to assign biological function to a list of genes. If you use multiple tools to get the same function, that's good. On the other hand, every tool has its own advantages and disadvantages, so you do not expect to get the same exact results.