GSEA for qPCR data
1
0
Entering edit mode
5.6 years ago
peter pfand ▴ 110

I have computed the differentially expressed genes in a qPCR experiment with ~600 genes. Now I need to perform a gene set enrichment analysis (GO) but do not know which set of genes I should use as the whole set of genes: the 600 genes used the qPCR array or all the genes in the genome given by the annotation?

The model is R and I'm using bioconductor.

GSEA GO qPCR • 1.5k views
ADD COMMENT
0
Entering edit mode
5.6 years ago

You should limit the background/whole set to what was analyzed/assayed. If not you will heavily bias in favor of sets you already selected multiple genes from and bias against sets you only selected 1 or 0.

ADD COMMENT

Login before adding your answer.

Traffic: 2297 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6