Hi Dick. (I've copied the aroma.affymetrix list in case others have the same question).
I remember doing an update *late* last year (don't remember exactly when) and recreating the CDFs --- the contents were identical to previous ones. That is, the Affymetrix annotation (at least how probesets are put into transcript clusters) doesn't change that much. I haven't checked recently -- do you know if Affy has made some major changes? If so, I'm happy to recreate them. But, just because they are dated July 2008, doesn't mean they have old information. However, if you use the Ensembl builds (for Exon 1.0ST), these change more regularly. The last one I built was Ensembl 50 and I see Ensembl is now at v54. In general, building CDFs for Exon arrays is described at: http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch Cheers, Mark On 12/06/2009, at 9:23 AM, dbe...@u.washington.edu wrote: > Hi Mark, > > I was wondering if there was any planned updates to the Mouse Exon 1.0 > ST cdf files? I noticed following your link: > http://groups.google.com/group/aroma-affymetrix/web/moex-1-0-st > that the last date was about a year ago. > > Or, if you could direct me to some document that would tell me how to > build custom cdfs, that would be good too. > > Thanks very much, > Dick > > On Aug 4 2008, 10:05 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote: >> Hi folks. >> >> I've been updating/creating CDF files for some of the recent >> Affymetrix "whole transcript" expression arrays (i.e. Human/Mouse/Rat >> Gene/Exon1.0 ST). You should be able to just download the relevant >> CDF, put it in the correct location (annotationData/chipTypes/.... as >> well as putting the data in the correct location) and run your >> standard sorts of analyses (e.g. BG correction, normalization, >> summarization, quality assessement) as described in the user's >> guide:http://groups.google.com/group/aroma-affymetrix/web/users-guide >> >> So far, I have created default versions, based on the Affymetrix >> (probeset CSV/unsupported CDF) annotation, for: >> >> Human Gene 1.0 >> SThttp://groups.google.com/group/aroma-affymetrix/web/hugene-1-0-st >> >> MouseGene 1.0 >> SThttp://groups.google.com/group/aroma-affymetrix/web/mogene-1-0-st-v1 >> >> Rat Gene 1.0 >> SThttp://groups.google.com/group/aroma-affymetrix/web/ragene-1-0-st-v1 >> >> MouseExon1.0 >> SThttp://groups.google.com/group/aroma-affymetrix/web/moex-1-0-st >> >> RatExon1.0 >> SThttp://groups.google.com/group/aroma-affymetrix/web/raex-1-0-st-v1 >> >> ... >> >> HumanExon1.0 ST has seen a little more development as Ken, Elizabeth >> and I all have worked directly with data from these, so we have some >> "custom" CDFs (and more on the way), based on different annotation >> sources. More information can be found at (and a big thank you to >> Elizabeth for the code that creates >> these):http://groups.google.com/group/aroma-affymetrix/web/huex-1-0-st-v2 >> >> If there are others on this list who want custom CDFs designed for >> any >> of these platforms, let me know and I can at least point you in the >> direction of how to create them. This is typically not a hard thing >> to do. >> >> Cheers, >> Mark ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
