[ensembl-dev] affy_hg_u133_plus_2 to ensg mappings

[Oliver Burren]

Hi,

I'm trying to retrieve all probset.id mappings to ensembl genes for 
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array 
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570) using ensmart 
71. However I noticed a large drop out wrt to the GEO annotation file so 
I did some digging...


If I look in Biomart for something like this


<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
			
	<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
		<Filter name = "affy_hg_u133_plus_2" value = "205332_at"/>
		<Attribute name = "ensembl_gene_id" />
		<Attribute name = "ensembl_transcript_id" />
	</Dataset>
</Query>

I get no results. However if I search the website for 205332_at and turn 
on the track for AFFY:HG-U133_Plus_2 it shows that the probeset (6 
features) maps to the gene. The help on this page 
http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html says 
' it is normally required that more than 50% of the probes in a probe 
set hit a given transcript sequence'. Is this the reason why this 
probeset isn't being tagged to this gene (although this appears to be 60%) ?

Any light that you could shed would be appreciated. Thanks,

Olly Burren


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