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.auwrote:
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
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