http://tech.groups.yahoo.com/group/GenePatternUserForum/ GenePattern Tue, 30 Sep 2008 16:52:31 GMT ted_liefeld http://tech.groups.yahoo.com/group/GenePatternUserForum/message/325 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/325 Sorry about the 'bad' sign-up link for the new forum, it seems to have moved here: http://wikiutils.nci.nih.gov/KC_signup Tue, 30 Sep 2008 16:51:10 GMT Dave Walton http://tech.groups.yahoo.com/group/GenePatternUserForum/message/324 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/324 When I follow the link to sign up to the new forum, I get an error page: Our apologies... The item you requested does not exist on this server or cannot be Tue, 30 Sep 2008 15:28:36 GMT ted_liefeld http://tech.groups.yahoo.com/group/GenePatternUserForum/message/323 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/323 To all GenePattern Forum members: We are transitioning the GenePattern user forum to a new server. The new forum can be found at Mon, 22 Sep 2008 08:58:27 GMT franzschaub http://tech.groups.yahoo.com/group/GenePatternUserForum/message/322 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/322 I would be happy to try the beta version of the new expression file creator. It would be great if you could inform me as soon it's ready. Franz ... custom cdf Fri, 19 Sep 2008 11:40:15 GMT marcdanie http://tech.groups.yahoo.com/group/GenePatternUserForum/message/321 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/321 Josh one of the GenePattern developers made a correction to the comment I made. Here is his response: ExpressionFileCreator does not currently support this Fri, 19 Sep 2008 11:34:31 GMT franzschaub http://tech.groups.yahoo.com/group/GenePatternUserForum/message/320 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/320 Thanks a lot for the help. I've now also provided the .cdf file for Human Gene ST 1.0 Array. However, I still get the same error: Error in just.rma(filenames = Thu, 18 Sep 2008 16:27:36 GMT marcdanie http://tech.groups.yahoo.com/group/GenePatternUserForum/message/318 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/318 To fix the problem in this case you will need to provide a custom cdf file. Marc-Danie Thu, 18 Sep 2008 14:54:18 GMT franzschaub http://tech.groups.yahoo.com/group/GenePatternUserForum/message/317 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/317 I'm using Affymetrix Human Expression Arrays (1.0 ST Arrays) and I tried to use the ExpressionfileCreator. My problem is, that the ExpressionFileCreator does Wed, 03 Sep 2008 21:11:11 GMT Michael Reich http://tech.groups.yahoo.com/group/GenePatternUserForum/message/316 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/316 Jeff, Thanks for this information. We'll make sure that the new module functionality is described in the module developer's guide also. Best, Michael ... -- Wed, 03 Sep 2008 18:42:53 GMT Jeff Gentry http://tech.groups.yahoo.com/group/GenePatternUserForum/message/315 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/315 Hi Michael ... I actually just deleted that message as not one minute after I sent that I stumbled across the information in the web client instructions Wed, 03 Sep 2008 18:00:26 GMT Michael Reich http://tech.groups.yahoo.com/group/GenePatternUserForum/message/314 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/314 Hi, If you haven't yet read our module developer's guide at http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_programmer.html, I recommend that Mon, 11 Aug 2008 09:19:29 GMT ted_liefeld http://tech.groups.yahoo.com/group/GenePatternUserForum/message/312 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/312 Stewart, it should be possible to do as you suggest but to my knowledge no one has yet tried it. Ted ... genepattern? If so it would be ... to..... ... Mon, 11 Aug 2008 08:59:49 GMT otagostewart http://tech.groups.yahoo.com/group/GenePatternUserForum/message/311 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/311 Hi, Is anyone out there using MySQL as a database backend for genepattern? If so it would be good to hear your experiences. I'm thinking it should be Sun, 27 Jul 2008 13:50:56 GMT sy_liang http://tech.groups.yahoo.com/group/GenePatternUserForum/message/310 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/310 Hi, I tried to follow the example (PepperExample.zip) given by PEPPeR GenePattern Quick Start Guide and was stuck by an error from LandmarkMatch under Tue, 17 Jun 2008 13:40:24 GMT marcdanie http://tech.groups.yahoo.com/group/GenePatternUserForum/message/309 http://tech.groups.yahoo.com/group/GenePatternUserForum/message/309 Nicolas, To create the res files to run in GenePattern you can run ExpressionFileCreator with the CEL files generated from Affymetrix. Regards, Marc-Danie