Dear list,
I was wondering the differences between annotation packages mogene20sttranscriptcluster.db and mogene21sttranscriptcluster.db. I assume that they are both related to MoGene ST 2.0 chip (couldn't find chip 2.1 in affymetrix site), but not sure what's new in mogene2.1 annotation file with respect to mogene 2.0.

Affymetrix just provides annotation for version 2.0 in its website and for the dataset mus musculus genes (GRCm38.p4), biomart provides as attribute ONLY Affy Mogene 2_1 probeset (not 2_0).

Is it just a matter of improved annotation info? Are the probe identifiers the same for mogene20sttranscriptcluster.db and mogene21sttranscriptcluster.db?

Thanks for your help,
Javier

I don't know about the updated annotations, but there is indeed a MoGene 2.1 array. The content is the same as on the 2.0 array, but the former is a so-called peg array (array organized in 96-well format; available per 16, 24 or 96 arrays for use in a GeneTitan system), whereas the later is a ("old fashioned style") cartridge array (available per 2, 6 or 30 as single arrays).

http://www.affymetrix.com/estore/catalog/131555/AFFY/Mouse+Gene+ST+Array+Plates#1_1

You should thus use the mogene20sttranscriptcluster.db annotations.

G