Affymetrix chip - unexpressed genes, which signal cuttof to use - (Dec/17/2007 )
Dear forum users,
I am using hgu133plus2 chips. I would like which intensity treshold should be used for filtering out genes that are not expressed at all.
To my knowledge,
Affymetrix produces its own present or absent call, by comparing the density coming from mismatch probes with that of perfect match probes.
So, rather than setting up a threshold, I would recommend having the present/absent calls. And then, eliminating the genes for which all the samples called absent.