[BioC] moe430v2 annotation package

[John Zhang]

>Thanks for the suggestion, that seemed to do the trick. Note that the 
>package is apparently called "moe430v2," which seems to be inconsistent 
>with how the probe and cdf packages are named ("mouse4302").

We actually have mouse4302 in the devel track. moe430v2 will go soon.

>
>Jeff.
>__________________________________
>Jeffrey Rasmussen
>Research Consultant, Bioinformatics
>Department of Immunology
>University of Washington
>__________________________________
>
>On Wed, 20 Oct 2004, James MacDonald wrote:
>
>> If you are using R-2.0.0, there is a devel version of moe4302 that you
>> can get using reposTools.
>>
>> library(reposTools)
>> install.packages2("moe4302", develOK=TRUE)
>>
>> You might compare this with what you got.
>>
>> HTH,
>>
>> Jim
>>
>>
>>
>> James W. MacDonald
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>>>> jeffrey rasmussen <rasmuss at u.washington.edu> 10/20/04 5:58 PM >>>
>> 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
>>
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>>
>>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084