Dear users, in case it is of help to anyone, just for the records or if someone can share some comments...

I have searched in the list for similar issue but have not found anything related.

We have just performed a Rat 2.0 Gene experiment and have found that current Affymetrix annotation files (version na34.rn5) have errors in the chromosome, strand, start and end columns. We got in touch with support and told us that there was an error in the annotation protocol and they will review it.

In addition to this, we have also detected that different transcript_cluster_IDs interrogate same genes/sequences, with apparently same probesets, so there is quite a degree of redundancy. On this, support has given us some explanations. Here just the start of the email:

"The short answer is that the re-use of probes with the
same sequence in different transcript clusters is a result of how the Gene
array design handles genes that have duplicate copies in different parts of the
genome, or genes that are part of a widespread gene family with regions of
near-identity. The issues regarding the gene assignments of these probes is a
side-effect of drift in the transcript record between array design and
annotation time. Read on for the
technical nitty-gritty.[...]

"

Finally, we have found that the Rat Gene 2.0 transcript annotation file , which has some 36000 transcript clusters i ntotal, has just below 30000 transcripts defined as "main", of which 11000 present no annotation whatsoever. Which to me is just too much lack of annotation.



HTH

Dave
 		 	   		  
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