Hi Sabrina.
I have not had to deal with this myself, but I do know that it exists
and I can at least suggest a possible route to exclude affected exons.
Presumably, there is a database (dbSNP?) that tells you the genome
locations of each SNP for your strains. There is also a probe.tab
file from Affymetrix that gives you the mapped genome locations of
each probe (or you could take the sequences from the same file and map
them yourself with a tool like BLAT). It is then just a matter of
looking whether each probe maps to a location on the genome that
overlaps a SNP. There is probably a Bioconductor tool for this or you
could create a hash, etc.
There are a couple levels at which you might introduce this to your
analysis. You could remove individual probes that are affected. On
the aroma.affymetrix side, this would require creating a new CDF with
those affected probes not included (a bit tricky but doable). Or, you
could simply post-process your existing results and remove probesets
that have an affected probe (easier but not as elegant).
You might've also seen:
Duan S, Zhang W, Bleibel WK, Cox NJ, Dolan ME: SNPinProbe 1.0: A
database for filtering out
probes in the Affymetrix GeneChip(R) Human Exon 1.0 ST array
potentially affected by SNPs.
Bioinformation 2008, 2(10):469{470.
Hope that gets you started.
Cheers,
Mark
On 30/04/2009, at 6:07 AM, sabrina wrote:
>
> Hi, all:
> I am using Aroma for detecting exon skipping events around two groups
> (two different strains). I found out that several of my top hits
> indeed includes at least one SNP between two strains. I wonder if
> anyone has some suggestion about how to deal with this situation. If I
> need to remove all affected exons from analysis, how can I do it? I
> never worked with SNP data before, can anyone give me a hint? Thanks a
> lot!
>
> Sabrina
> >
------------------------------
Mark Robinson
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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