[BioC] only 9-digit refseq IDs when using custom CDF for mouse4302 array

Jarek Bryk bryk at evolbio.mpg.de
Fri Sep 25 14:37:11 CEST 2009


I am not sure if this is a problem, but here we go. When I analyse my 
Affy mouse4302 data using custom CDF file from the Dai lab that 
collapses probe/sets onto RefSeq IDs:

 > affy.batch.object at cdfName<-"Mouse4302_Mm_REFSEQ"

I only get 9-digit RefSeq IDs, and none of the more common 6-digit IDs. 
Maybe I am missing something, but it seems a bit strange to get this 
bias and I wonder why could it be so? There is no apparent difference 
between the 6- and 9-digit IDs on the GenBank side, as far as I can tell.

I would be very grateful for any clues,

   Jarek Bryk
   Max Planck Institute for Evolutionary Biology
   August Thienemann Str. 2 | 24306 Plön, Germany
   tel. +49 4522 763 287 | bryk at evolbio.mpg.de

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