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 [[alternative HTML version deleted]]

Hi Dave, This is of interest to me since these Affy files are what we use to make annotation packages. Here we are faced every release with the reality that our packages can only be as good as the original files. So to the extent that you successfully lobby Affymetrix to improve them, we will also be able to also improve our probe and chip packages based on that platform. So thanks for caring enough to talk to Affy about it! The entire community can benefit if you get them to improve things. Marc On 07/24/2014 08:04 AM, David wrote: > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor