Hi Sabrina.
Comments below.
On 06/06/2009, at 1:57 AM, sabrina wrote:
>
> Hi, Mark:
> I finally found the SNP data set that is suitable for my case. As I
> understand, aroma used RMA to estimate gene level and exon level
> intensities. After I estimate gene level (transcript level), I can use
> FIRMA to estimate residual for each exon and compose a score as
> described in the paper . My question is: if there is a SNP difference
> between two strains within one exon, should I exclude that exon from
> estimating transcript level value? My guess is probably no.
If the SNP affects only 1 probe in an entire transcript, I would
expect it to have very little impact on the gene-level summary. And,
especially so if there are a large number of total probes for that
gene. It may have a noticeable effect on the probe effect.
> So will it
> be a good idea if I exclude that exon after I calculate all FIRMA
> scores or should I exclude these exons after I estimate residuals ,
> but only used these residuals not affected by SNPs for firma score
> estimation? Thanks
Keep in mind the residuals are calculated at the probe-level, not the
probeset-level. The FIRMA score is then a summary of the all the
residuals for a probeset.
I think you have (at least) 3 choices:
1. (preferred, i would think) you could remove all affected *probes*
(via the creation of a SNP-affected-probe-free CDF) in advance, then
run FIRMA as normal. I can help with this if you tell me which probes
are affected.
2. remove the affected *probesets* afterwards, since you may not
believe the FIRMA scores for which these are based on.
3. as you suggested, only calculate FIRMA scores from unaffected
residuals. But, the information you require to do this is the same
information required to do #1 and it would seems like #1 is preferred.
The good thing about option #1 is you would still have some ability to
detect differential splicing for the probeset (instead of tossing it
away), albeit with the smaller number of remaining unaffected probes.
Cheers,
Mark
> Sabrina
>
> On Apr 30, 3:46 am, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>> 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) HumanExon1.0 ST array
>> potentially affected bySNPs.
>> 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 detectingexonskipping 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
>> ------------------------------
> >
------------------------------
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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