[BioC] moe430v2 annotation package

[jeffrey rasmussen]

I am trying to build an annotation package for Affy's Moe430 2.0 array 
(since it does not appear to be available under the metadata section) and 
I am wondering if my approach is the same as is used to build the 
"official" metadata packages.

What I did was to simply use the annotation available from Affymetrix to 
map each probe id to its corresponding genbank id using the file:
http://www.affymetrix.com/Auth/analysis/downloads/taf/Mouse430_2_annot_csv.zip
and then run ABPkgBuilder as detailed in the vignette "How to use 
AnnBuilder."

The reason for my concern is that the QC stats my efforts returned 
indicate that I have fewer probes annotated then the sum of the QC stats 
for the moe430a and moe430b packages would give me.

Here's what my moe430_2QC.rda contains:

Quality control information for  moe430_2
Date built:  Wed Oct 20 13:46:14 2004
Number of probes: 45102
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
          moe430_2ACCNUM found 45102 of 45102
          moe430_2CHR found 31093 of 45102
          moe430_2CHRLOC found 21050 of 45102
          moe430_2ENZYME found 1469 of 45102
          moe430_2GENENAME found 31297 of 45102
          moe430_2GO found 17752 of 45102
          moe430_2GRIF found 0 of 45102
          moe430_2LOCUSID found 31362 of 45102
          moe430_2MAP found 28106 of 45102
          moe430_2OMIM found 0 of 45102
          moe430_2PATH found 2757 of 45102
          moe430_2PMID found 29071 of 45102
          moe430_2REFSEQ found 25512 of 45102
          moe430_2SUMFUNC found 0 of 45102
          moe430_2SYMBOL found 31298 of 45102
          moe430_2UNIGENE found 30800 of 45102
Mappings found for non-probe based rda files:
          moe430_2CHRLENGTHS found 21
          moe430_2ENZYME2PROBE found 387
          moe430_2GO2ALLPROBES found 4483
          moe430_2GO2PROBE found 3252
          moe430_2ORGANISM found 1
          moe430_2PATH2PROBE found 122
          moe430_2PMID2PROBE found 21108

However, for example, the sum of moe430aGO (found 15262 of 22690) and 
moe430bGO (found 4499 of 22575) listed under the metadata section 
indicates that merging these two packages --after all, the moe430 2.0 
array is just that, a merge of the A and B chips-- would give me more 
annotations than my efforts produced, which is unexpected given that the 
moe430a and moe430b packages were created > 6 months ago. Has something 
changed within the AnnBuilder package (I'm using version 1.4.18 under 
linux) or the sources used for annotation (I used getSrcUrl("all", 
organism="Mus Musculus") to src the various annotation files) that would 
explain these results?

Best,
Jeff
__________________________________
Jeffrey Rasmussen
Research Consultant, Bioinformatics
Department of Immunology
University of Washington