http://tech.groups.yahoo.com/group/customcdf/ custom CDF Fri, 18 Dec 2009 11:10:29 GMT tfrayner http://tech.groups.yahoo.com/group/customcdf/message/136 http://tech.groups.yahoo.com/group/customcdf/message/136 Hi Manhong, Marvellous, thank you very much. I'd been making exactly the same error, and switching rows for columns does indeed solve the problem. Best Fri, 18 Dec 2009 04:36:47 GMT jkevinwang http://tech.groups.yahoo.com/group/customcdf/message/135 http://tech.groups.yahoo.com/group/customcdf/message/135 Hi Manhong, After updating my rma package to 1.24.2, the problem was solved. Thanks for your help. Kevin Wed, 16 Dec 2009 21:29:08 GMT daimh@... http://tech.groups.yahoo.com/group/customcdf/message/134 http://tech.groups.yahoo.com/group/customcdf/message/134 Dear Custom CDF/WGAS User, Thanks to Dr Tim Rayner in Cambridge, we found a problem for chip HuGene11stv1 in Custom CDF R packages. Those packages for this Wed, 16 Dec 2009 17:40:38 GMT Manhong Dai http://tech.groups.yahoo.com/group/customcdf/message/133 http://tech.groups.yahoo.com/group/customcdf/message/133 Hi Tim, Thank you for letting me know this problem. It turned out to be the chip size is 990x1190. When we built custom CDF for this chip, it is not released Wed, 16 Dec 2009 16:49:53 GMT tfrayner http://tech.groups.yahoo.com/group/customcdf/message/132 http://tech.groups.yahoo.com/group/customcdf/message/132 Hi, ... Error in .local(object, ...) : subscript out of bounds This problem also occurs with the example CEL files available on Affy's web site. I've Wed, 16 Dec 2009 14:33:54 GMT Manhong Dai http://tech.groups.yahoo.com/group/customcdf/message/131 http://tech.groups.yahoo.com/group/customcdf/message/131 Hi Kevin, I tested your command under my environment (R 2.10.0; affy 1.24.2; CustomCDF 1.1.0), it works for me. ... Warning message: In Tue, 15 Dec 2009 05:09:54 GMT jkevinwang http://tech.groups.yahoo.com/group/customcdf/message/130 http://tech.groups.yahoo.com/group/customcdf/message/130 Hi Manhong, I encountered an error when I ran the rma function on an Affybatch object generated from read.affybatch.hybrid. I have 6 CEL files, 3 based on the Tue, 15 Dec 2009 05:02:12 GMT jkevinwang http://tech.groups.yahoo.com/group/customcdf/message/129 http://tech.groups.yahoo.com/group/customcdf/message/129 Hi Mahong, Thanks for the prompt reply. Yes, the error occurred when I tried to install it to a Windows machine. I realized that the source code was only for Mon, 14 Dec 2009 14:53:47 GMT Manhong Dai http://tech.groups.yahoo.com/group/customcdf/message/128 http://tech.groups.yahoo.com/group/customcdf/message/128 Hi Kevin, This version is the latest. The thing is it supports Linux/Unix platform only. Are you installing it under Linux? if so, what is the error message Mon, 14 Dec 2009 07:24:19 GMT Kevin Wang http://tech.groups.yahoo.com/group/customcdf/message/127 http://tech.groups.yahoo.com/group/customcdf/message/127 Hi, Can someone please let me know the latest link for downloading the CustomCDF R package? I could not successfully install the R package downloaded from Fri, 04 Dec 2009 13:39:22 GMT Christoph Jüschke http://tech.groups.yahoo.com/group/customcdf/message/126 http://tech.groups.yahoo.com/group/customcdf/message/126 Hi Manhong, thank you for your reply. It would be great if you could include FlyBase transcript IDs in version 13. When I do the re-mapping of the Affymetrix Thu, 03 Dec 2009 18:21:37 GMT Manhong Dai http://tech.groups.yahoo.com/group/customcdf/message/125 http://tech.groups.yahoo.com/group/customcdf/message/125 Hi Christoph, We can include flybase Transcripts in version 13, or do you prefer other type? If you want to create it, I would suggest to generate a flat CDF Wed, 02 Dec 2009 18:25:21 GMT daimh@... http://tech.groups.yahoo.com/group/customcdf/message/124 http://tech.groups.yahoo.com/group/customcdf/message/124 Dear Custom CDF/WGAS User, Custom cdf packages version 12.0.0 is just upgraded to 12.1.0, in order to be compatible with R 2.10.z and Bioc 2.5. You've received Tue, 01 Dec 2009 11:52:12 GMT Christoph Jüschke http://tech.groups.yahoo.com/group/customcdf/message/123 http://tech.groups.yahoo.com/group/customcdf/message/123 Hello, In the Drosophila community we mostly use FlyBase as our favourite database for genes and transcripts since it is very well annotated. Is there a Mon, 09 Nov 2009 19:02:02 GMT Manhong Dai http://tech.groups.yahoo.com/group/customcdf/message/122 http://tech.groups.yahoo.com/group/customcdf/message/122 Hi Denise, We only uses two files from Affymetrix to build custom CDF, one is cdf file, which has the mapping between probeset and probe, the other is sequence