[BioC] problem with MOE430a annotation & NetAffx correspondence

John Zhang jzhang at jimmy.harvard.edu
Fri Jul 30 21:42:16 CEST 2004

>I spotted a weird problem with the annotation in moe430a arrays.
>If you use
>getLL("1427131_s_at","moe430a") you get 11461 which correspond to actb 
>gene (actib beta)
>But if you go to NetAffx and query for the same probeID you get a 
>completely different gene (Riken)

When I traced our mappings back to the source file, I noticed that Mm.data.gz 
file from Unigene has an entry "LOCUSLINK   320184; 11461" for the GenBank 
Accession number of the probe. Our system picks the smallest LocusLink id when 
there is are conflicts and if we do not know which one to trust more. That was 
how we ended up with 11461 rather than 320184, which is an RIKEN gene. 

I have writen to UniGene about the mapping and will see what we should do when I 
hear from them.


>What's going on? Any idea?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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