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. ______________________________________________________________________ -- 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/