<html><head><base href="x-msg://145/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Currently the code does not support differing sizes for the same probeset across arrays. The default behaviour is to take the largest size.</div><div><br></div><div>This tends not to occur with commercial arrays and the warning you are seeing is there as a safe guard, such that the user is aware when non-standard array design is loaded.</div><div><br></div><div>Nath</div><div><br></div><div><br></div><div><br></div><br><div><div>On 13 Sep 2010, at 13:49, Oliver, Gavin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-US" link="blue" vlink="purple"><div class="Section1" style="page: Section1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Hi all,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">I have just started probe2transcript for 6 custom arrays and the first output I got was a series of messages about probesets with the same name having different numbers of probes on the arrays.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Now, I know what the message means and I know of the existence of these probesets (they are intentionally created like this).<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Why question is – how will<span class="Apple-converted-space"> </span><a href="http://probe2transcript.pl" style="color: blue; text-decoration: underline; ">probe2transcript.pl</a><span class="Apple-converted-space"> </span>actually treat them? Can I expect annotation problems for these probesets??<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Best,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Gavin<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><font face="Tahoma" size="2"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><strong><b><span style="font-size: 12pt; color: blue; "><font face="Times New Roman"> </font></span></b></strong></div><strong><b><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font color="#000000"><span lang="EN-GB" style="font-family: 'Times New Roman'; ">The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font color="#0000ff"><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Group (UK) Limited, registered no. NI061368.<span> <span class="Apple-converted-space"> </span></span>Almac Sciences Limited, registered no. NI041550.<span> <span class="Apple-converted-space"> </span></span>Almac Discovery Limited, registered no. NI046249.<span class="Apple-converted-space"> </span><span> </span>Almac Pharma Services Limited, registered no. NI045055.<span> <span class="Apple-converted-space"> </span></span>Almac Clinical Services Limited, registered no. NI041905.<span> <span class="Apple-converted-space"> </span></span>Almac Clinical Technologies Limited, registered no. NI061202.<span class="Apple-converted-space"> </span><span> </span>Almac Diagnostics Limited, registered no. NI043067.<span> <span class="Apple-converted-space"> </span></span>All preceding companies are registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on">Northern Ireland</st1:country-region><span class="Apple-converted-space"> </span>with a registered office address of Almac House, 20 Seagoe Industrial Estate,<st1:place w:st="on"><st1:city w:st="on">Craigavon</st1:city>,<span class="Apple-converted-space"> </span><st1:postalcode w:st="on">BT63 5QD</st1:postalcode>,<span class="Apple-converted-space"> </span><st1:country-region w:st="on">UK</st1:country-region></st1:place>.<span class="Apple-converted-space"> </span><span> </span><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region><span class="Apple-converted-space"> </span>no. SC154034.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are<span class="Apple-converted-space"> </span><st1:state w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:state><span class="Apple-converted-space"> </span>limited liability companies and Almac Group Incorporated is a Delaware Corporation.<span> <span class="Apple-converted-space"> </span></span>More information on the Almac Group can be found on the Almac website:<a href="http://www.almacgroup.com" style="color: blue; text-decoration: underline; ">www.almacgroup.com</a><o:p></o:p></span></div></b></strong></font>_______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline; ">Dev@ensembl.org</a><br><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: blue; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br></div></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Email: <a href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">TelNo: (+44)1223 492629</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span><br class="Apple-interchange-newline">
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