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.
>> ______________________________________________________________________
>>
>
>
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