<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
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
(<a class="moz-txt-link-freetext" href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570">http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570</a>) using
ensmart 71. However I noticed a large drop out wrt to the GEO
annotation file so I did some digging...<br>
<br>
<br>
If I look in Biomart for something like this <br>
<br>
<br>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<pre style="color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;"><?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>
</pre>
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
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html">http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html</a>
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%) ?<br>
<br>
Any light that you could shed would be appreciated. Thanks,<br>
<br>
Olly Burren<br>
<br>
<br>
</body>
</html>