Question: GSEA for qPCR data
gravatar for peter pfand
3.8 years ago by
peter pfand80
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 • 1.2k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 3.8 years ago by peter pfand80
gravatar for WouterDeCoster
3.8 years ago by
WouterDeCoster42k 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 3.8 years ago • written 3.8 years ago by WouterDeCoster42k
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