Hi Qicheng. Definitely ENSG, as that will use all the probes for all transcripts.
Cheers, Mark On 2010-08-31, at 10:59 AM, Qicheng Ma wrote: > Hi Mark, > > I looked at their customCDF file, I feel it would be easier to use > their CDF file and modify the transcript annotation and probe sequence > files than to modify the Affy CDF file. However, they provide CDF files to > both genes (ENSG) and transcripts (ENST). > > Could you tell me whether it make more sense to use CDF for ENSG or > CDF for ENST for alternative splicing analysis with exon arrary by FirmaGene ? > > Thanks, > > Qicheng > > On Sun, Aug 29, 2010 at 9:25 PM, Qicheng Ma <qicheng...@gmail.com> wrote: > Hi Mark, > > Thank for your quick reply. If I can make a custom CDF myself according > to FirmaGene requirement: > > 1)need a CDF file where all the probes (cells) are within 1 group ... AND, > 2)need to ensure that the order of the probes is the order in which they map > to the genome/transcript. > > what kind of info do I need to extract from the HuEx-1_0-st-v2,coreR3, > A20071112,EP.cdf file to satisfy those two requirement. > > Thanks again, > > Qicheng > > > On Sun, Aug 29, 2010 at 7:39 PM, Mark Robinson <mrobin...@wehi.edu.au> wrote: > Hi Qicheng. > > I don't think that particular CDF will work with FIRMAGene, since it is laid > out in a list of lists (probes -- "cells", for probe selection regions or > "groups" -- are laid out within transcript clusters -- "units"). The > cell/group/unit are CDF speak. > > Basically, in order for FIRMAGene to work (and note that I haven't run > FIRMAGene on the Exon platform myself), you need a CDF file where all the > probes (cells) are within 1 group ... AND, you need to ensure that the order > of the probes is the order in which they map to the genome/transcript. This > is what FIRMAGene assumes. > > I believe the CDF files created by brainarray: > > http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp > > ... are organized this way, but you'd have to verify that for yourself. > > Hope that gets you started. > > Cheers, > Mark > > On 2010-08-27, at 6:36 AM, Qicheng Ma wrote: > > > Hi Mark, > > > > Could you please tell me whether we can run FirmaGene > > (http://bioinf.wehi.edu.au/folders/firmagene/sup3_04feb2010.R) on human > > exon array using CDF file HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf , since > > FirmaGene score would be more useful than Firma score from individual exons > > ? > > > > Thanks, > > > > Qicheng > > ------------------------------ > 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 > ------------------------------ > > > > > > > ______________________________________________________________________ > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of the > sender. > ______________________________________________________________________ > > ------------------------------ 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 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
