[BioC] Annotations dealing with "removed" refseq record
fpepin at cs.mcgill.ca
Fri Jun 8 22:31:30 CEST 2007
I think the annotation system has problems dealing with RefSeq that were
This is looking at the Erbb2 gene in mouse (entrezID=13866) on the whole
genome mouse chip from Agilent (annotation package: mgug4122a). From the
annotations provided by Agilent, there are 2 probes that map to it:
A_52_P49250 and A_51_P216179.
Currently, the annotations do not give any results for it:
The accession number that is given indeed points to NM_010152.
Looking at it on the NCBI website, it does point to Erbb2, but it also
says: "This record was removed by RefSeq staff".
Not being entirely familiar with the process, I would point to this as a
likely reason for the lack of annotations for those two probes.
I have not done an extensive check between the Agilent annotation and
the ones in mgug4122a to see how many other probes might be hit by this.
R version 2.5.0 (2007-04-23)
attached base packages:
 "stats" "graphics" "grDevices" "utils" "datasets"
 "methods" "base"
other attached packages:
If there is any more information I can provide, please tell
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