<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Eduardo<div><br></div><div>Just for completeness, and anyone else pondering the answer to this, I am replying in brief, to the list also.</div><div><br></div><div>As I said, the problem here is that you need to look at the probe level for non-affy arrays. Transcript xrefs are associated with probesets for affy arrays and probes for non-affy arrays.</div><div><br></div><div>Thanks</div><div><br></div><div>Nath</div><div><br><div><div>On 17 Jun 2011, at 11:44, Eduardo Andrés León wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear all,<div><br></div><div>I'm using this code :</div><div><br></div><div><div><i>my $tx_adaptor = $registry->get_adaptor("human","core","Transcript");</i></div><div><i>my $ps_adaptor = $registry->get_adaptor("human","funcgen","ProbeSet");</i></div><div><i><br></i></div><div><i>#Fetch the transcript and associated ProbeSets</i></div><div><i>my $transcript = $tx_adaptor->fetch_by_stable_id(ENST00000381223);</i></div><div><i>my @probesets = @{$ps_adaptor->fetch_all_by_external_name($transcript->stable_id)};</i></div><div><i>foreach my $probeset (@probesets){</i></div><div><span class="Apple-tab-span" style="white-space:pre"><i> </i></span><i>my $arrays = $probeset->get_all_Arrays();</i></div><div><span class="Apple-tab-span" style="white-space:pre"><i> </i></span><i>foreach my $probe (@$arrays){</i></div><div><span class="Apple-tab-span" style="white-space:pre"><i> </i></span><i>print "\t". $probeset->name ."\t" . $probe->name() ."\n";</i></div><div><span class="Apple-tab-span" style="white-space:pre"><i> </i></span><i>}</i></div><div><i>}</i></div></div><div><br></div><div>To find all probes related with a transcript (for example : ENST00000381223) .</div><div><br></div><div>in the page , the results is something like :</div><div><br></div><div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/Oligos?db=core;g=ENSG00000214717;r=X:2404455-2419008;t=ENST00000381223">http://www.ensembl.org/Homo_sapiens/Transcript/Oligos?db=core;g=ENSG00000214717;r=X:2404455-2419008;t=ENST00000381223</a></div><div><br></div><div>where 11 platforms are found :</div><div><i><p style="display: inline !important; "><strong><br></strong></p></i></div><div><i><p style="display: inline !important; "><strong>This transcript corresponds to the following database identifiers:</strong></p></i></div><div><i><table cellpadding="4"><tbody><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AFFY HG-U133_Plus_2:</strong></th><td><div class="multicol">1554821_a_at<span class="small">[11/11 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=1554821_a_at;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">203043_at<span class="small">[9/11 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=203043_at;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AFFY HG-U95A:</strong></th><td><div class="multicol">39168_at<span class="small">[16/16 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=39168_at;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AFFY HG-U95B:</strong></th><td><div class="multicol">44978_at<span class="small">[16/16 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=44978_at;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AFFY HuEx-1_0-st-v2:</strong></th><td><div class="multicol">3997567<span class="small">[4/4 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997567;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">3997568<span class="small">[4/4 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997568;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">3997569<span class="small">[4/4 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997569;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">3997570<span class="small">[4/4 in probeset. Matches 3 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997570;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">3997571<span class="small">[4/4 in probeset. Matches 3 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997571;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">3997575<span class="small">[4/4 in probeset. Matches 6 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997575;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">3997576<span class="small">[4/4 in probeset. Matches 6 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=3997576;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">4033358<span class="small">[4/4 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=4033358;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">4033359<span class="small">[4/4 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=4033359;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">4033360<span class="small">[4/4 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=4033360;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">4033361<span class="small">[4/4 in probeset. Matches 3 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=4033361;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">4033362<span class="small">[3/3 in probeset. Matches 3 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=4033362;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">4033365<span class="small">[4/4 in probeset. Matches 6 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=4033365;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AFFY HuGene-1_0-st-v1:</strong></th><td><div class="multicol">8171139<span class="small">[32/42 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=8171139;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">8177029<span class="small">[22/42 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=8177029;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AFFY U133_X3P:</strong></th><td><div class="multicol">Hs2.9933.2.S1_3p_x_at<span class="small">[11/11 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=Hs2.9933.2.S1_3p_x_at;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">g4759257_3p_at<span class="small">[9/11 in probeset. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=g4759257_3p_at;ptype=pset;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>AGILENT WholeGenome:</strong></th><td><div class="multicol">A_23_P217507<span class="small">[Matches exon/3' flank boundary. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=A_23_P217507;ptype=probe;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div><div class="multicol">A_32_P86623<span class="small">[Matches exon/3' flank boundary. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=A_32_P86623;ptype=probe;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>CODELINK:</strong></th><td><div class="multicol">GE53488<span class="small">[Matches 3' flank. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=GE53488;ptype=probe;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>ILLUMINA HumanWG_6_V2:</strong></th><td><div class="multicol">ILMN_1694466<span class="small">[Matches 3' flank. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=ILMN_1694466;ptype=probe;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr><tr><th style="white-space: nowrap; padding-right: 1em;"><strong>PHALANX OneArray:</strong></th><td><div class="multicol">PH_hs_0026388<span class="small">[Matches exon/3' flank boundary. Matches 2 other transcripts]</span> [<a href="http://www.ensembl.org/Homo_sapiens/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSG00000214717;id=PH_hs_0026388;ptype=probe;r=X:2404455-2419008;t=ENST00000381223">view all locations</a>]</div></td></tr></tbody></table><div><br></div></i></div><div><i> But in my case only</i></div><div><br></div><div><div><span class="Apple-tab-span" style="white-space:pre"> </span>44978_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U95B</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>39168_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U95Av2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>39168_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U95A</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Hs2.9933.2.S1_3p_x_at<span class="Apple-tab-span" style="white-space:pre"> </span>U133_X3P</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>203043_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-Focus</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>203043_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U133A_2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>203043_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U133A</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>203043_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U133_Plus_2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>g4759257_3p_at<span class="Apple-tab-span" style="white-space:pre"> </span>U133_X3P</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>1554821_a_at<span class="Apple-tab-span" style="white-space:pre"> </span>HG-U133_Plus_2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997575<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997569<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997571<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997568<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997570<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>4033360<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>4033365<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>4033359<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>4033358<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>4033362<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997567<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>4033361<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>3997576<span class="Apple-tab-span" style="white-space:pre"> </span>HuEx-1_0-st-v2</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>8171139<span class="Apple-tab-span" style="white-space:pre"> </span>HuGene-1_0-st-v1</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>8177029<span class="Apple-tab-span" style="white-space:pre"> </span>HuGene-1_0-st-v1</div><div><br></div><div>What do I have to do to find the AGILENT WholeGenome and ILLUMINA HumanWG_6_V2 probes ???</div></div><div><br></div><div>Thank you in advance.</div><div><strong><br></strong></div><div><br></div><div><div>
===================================================<br>Eduardo Andrés León<br>Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 5054)<br>e-mail: <a href="mailto:eandres@cnio.es">eandres@cnio.es</a> Fax: (+34) 91 224 69 76<br>Unidad de Bioinformática Bioinformatics Unit<br>Centro Nacional de Investigaciones Oncológicas<br>C.P.: 28029 Zip Code: 28029<br>C/. Melchor Fernández Almagro, 3 Madrid (Spain)<br><a href="http://bioinfo.cnio.es/">http://bioinfo.cnio.es</a><span class="Apple-tab-span" style="white-space: pre; "> </span><a href="http://bioinfo.cnio.es/people/eandres">http://bioinfo.cnio.es/people/eandres</a><br>===================================================
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