[BioC] codelink database submission IDs changing

Matthew Neville matthew.neville at oxlip.ox.ac.uk
Mon Jul 6 20:39:08 CEST 2009


has anyone had any problems with the annotation or codelink data once  
exported from the Codelink App, i.e. changing accession IDs.

I apologise in advance for not having the codelink version number to  
hand but can't access my laptop at the moment.
I am running the Codelink app to normalise my Human whole genome  
codelink arrays.  In the first week in June I updated R, Bioconductor,  
and Codelink to get the latest versions on my Mac OSX10.5.  One month  
in I have discovered that some very important genes are missing from  
my "writecodelink" export file.  More accurataly, it appears that the  
latest annotaion database has re-assigned over 8000 of the IDs.  Some  
are an improvement, from NAs to a database number but many have re- 
assigned a NM_ id to an est ID such as BG... or AK....  There is no  
wrong gene asignments but the est IDs are not recognised by my  
downstream analysis software.  Is there a reason for this or is it a  
database glitch


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