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<div class="moz-cite-prefix">Hi Nathan,<br>
<br>
Thanks a lot for the reply - very helpful. I was trying to add
ENSG id's (E71) to the GEO annotation file available for this
platform. I expected some drop out (due to annotation differences
etc) but wasn't expecting ~9000 protein coding genes (14000
probesets) to go missing between GEO and ensembl. I guess a more
stringent QC strategy would probably explain do that, I was
worried that there was a problem with my way of doing this, but
this doesn't seem to be the case.<br>
<br>
Thanks for your help.<br>
<br>
Olly<br>
<br>
On 17/06/13 21:39, Nathan Johnson wrote:<br>
</div>
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cite="mid:074560E5-3FCB-42AD-B57E-0E819DC80CD4@ebi.ac.uk"
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Hi Oliver
<div><br>
</div>
<div>The reason why this isn't being considered as a transcript
xref is because it is on the wrong strand. This is an easy
mistake to make as many of the array technologies differ in how
they process the RNA sample and hence what strand is actually
hybridised when it eventually meets the array.</div>
<div><br>
</div>
<div>There is a digram of the IVT processing on this page:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_1">http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_1</a></div>
<div><br>
</div>
<div>In saying that, that particular set of alignments does look
like it was designed for the exons of that gene, albeit with
some exon boundary overlap. However, IVT arrays normally target
3' ends and UTRs specifically, which makes this particular
probeset even more odd.</div>
<div><br>
</div>
<div> Sorry I can't be of more help.</div>
<div><br>
</div>
<div>Nathan</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On 17 Jun 2013, at 15:58, Oliver Burren <<a
moz-do-not-send="true"
href="mailto:oliver.burren@cimr.cam.ac.uk">oliver.burren@cimr.cam.ac.uk</a>>
wrote:</div>
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<div 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 moz-do-not-send="true"
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>
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<pre style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; 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 moz-do-not-send="true"
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>
</div>
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