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:


... are organized this way, but you'd have to verify that for yourself.

Hope that gets you started.


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

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