Transferring Affymetrix Probesets To Entrez gene Ids
Entering edit mode
7.4 years ago

Hi, I have some gene signatures composed by probset names (HGU133plus 2.0) and I would like to transfer them in a format suited for TCGA RNAseq (Colon and rectal adenocarcinomas). TCGA level 3 genes annotation is "gene Symbol/ Entrez", so ideally I should be able to map the "probset name" to the "Entrez id" in a reliable way. I know that it's possible in R using the Bioconductor library hgu133plus2.db but I'm wondering if that is the best way and the most reliable one.

I found that the probeset annotation from affymetrix could be not so accurate since the evolution of the biological knowledge and the technology. There are several authors pointing out the necessity of probesets re-annotation starting from the probes level. Is this true also for the annotation at probset names -> gene ids level? Is hgu133plus2.db accuarte and reliable?


RNA-Seq probesets affymetrix entrez genes • 1.8k views

Login before adding your answer.

Traffic: 2468 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6