[BioC] Missing ProbeSets in Affymetrix MoGene 1.0 ST chips

[James W. MacDonald]

Have you asked anybody at Affy?

Mark Cowley wrote:
> Dear list,
> There are 93 transcript_cluster_id's on the MoGene 1.0 ST chip that are 
> listed in the csv annotation file, and searchable in the MoGene chip at 
> NetAffx, but that are not present in the [unsupported] CDF file from 
> netaffx.
> 45 of these ID's are present in the MoGene PGF file, and correspond to 
> the antigenomic probesets, but the remaining 48 are not in the PGF file 
> either.
>  From NetAffx, the 48 non-control probesets are: 11 snRNA's, a RefSeq 
> gene (Lphn2) and 2 other novel transcripts, with the remaining 44 having 
> no annotation other than their genomic location. This isn't a problem, 
> unless Lphn2 is your gene of interest, which it isn't in my case, but it 
> would be nice to know what's going on here!
> 
> If you RMA normalise using the CDF file (like genespring does) then you 
> end up with 93 rows of missing data, or if you normalise using the 
> PGF/CLF files then you will end up missing out on the remaining 48 
> probesets.
> 
> Has anyone else come across this and know what is going on here??
> 
> These transcript_cluster_ids are:
> c("10361826", "10362430", "10362444", "10362452", "10502768", 
> "10532622", "10349381", "10350469", "10354866", "10362438", "10362872", 
> "10369759", "10374030", "10391748", "10395778", "10411504", "10422960", 
> "10436496", "10436660", "10446349", "10453719", "10457089", "10458079", 
> "10460144", "10461932", "10481652", "10482786", "10487009", "10498317", 
> "10501216", "10502040", "10503414", "10513713", "10521665", "10535929", 
> "10546555", "10552810", "10553535", "10560364", "10582560", "10582566", 
> "10582570", "10582576", "10585872", "10586931", "10592453", "10601614", 
> "10602194", "10338002", "10338005", "10338006", "10338007", "10338008", 
> "10338009", "10338010", "10338011", "10338012", "10338013", "10338014", 
> "10338015", "10338016", "10338018", "10338019", "10338020", "10338021", 
> "10338022", "10338023", "10338024", "10338027", "10338028", "10338030", 
> "10338031", "10338032", "10338033", "10338034", "10338038", "10338039", 
> "10338040", "10338043", "10338045", "10338046", "10338048", "10338049", 
> "10338050", "10338051", "10338052", "10338053", "10338054", "10338055", 
> "10338057", "10338058", "10338061", "10338062")
> 
> cheers,
> Mark
> -----------------------------------------------------
> Mark Cowley, BSc (Bioinformatics)(Hons)
> 
> Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662