Question: GSEA for qPCR data
0
gravatar for peter pfand
3.1 years ago by
peter pfand80
Germany
peter pfand80 wrote:

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 qpcr go • 1.0k views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 3.1 years ago by peter pfand80
0
gravatar for WouterDeCoster
3.1 years ago by
Belgium
WouterDeCoster38k wrote:

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 COMMENTlink modified 3.1 years ago • written 3.1 years ago by WouterDeCoster38k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 936 users visited in the last hour