probeset mapping to multiple entrezIDs

Question

[BrunoGiotti]

Hello,

Hope someone can help me on this. Basically I'm mapping probeIDs from the chip hgu133a.db to entrezIDs and I found that out of 22283 probesetIDs, 1266 maps to multiple entrezIDs. within it there are microRNAs, histones, pseudogenes and other weird stuff :D. So question is...how do I make the call, if it is possible, to which is the most reliable mapping for each of the multimapping probeset?

Hope this question is pertinent to this community.

Thank you
Bruno
PhD student in Genomics
Roslin Institute, Scotland

Answer 1

[Sean Davis]

A common approach is to ignore (remove) probesets that map to multiple genes. Another approach is to simply treat the probesets as "measurements", do your differential expression analysis, and if one of these multi-mapping probesets shows up as "important", dig into the annotation for that probeset specifically by hand.

[BrunoGiotti]

thanks! I think I'm going to remove them as I need to bind different datasets using EntrezIDs as reference.