[BioC] Missing ProbeSets in Affymetrix MoGene 1.0 ST chips

[Mark Cowley]

no, not yet! I will do now.

On 04/09/2008, at 10:52 PM, James W. MacDonald wrote:

> 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
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