Out of curiosity (primarily for Alejandro, Simon, Wolfgang et al.) -- how
easy/difficult would it be to tweak the plotExons function in DEXSeq so
that it takes advantage of Gviz functionality?  I could see this being
obscenely powerful.

Lately I have been writing a lot of coercions to/from SummarizedExperiment
objects, mostly so that grouping and subsetting of features for Gviz are
nearly automatic.  (Well, that, and preparing things for publication ;-))
 DEXSeq has one of the cooler plots around, and (IIRC) it takes advantage
of some of the same data structures as Gviz would -- have you (plural, at
EMBL) gauged how easy/hard and worthwhile/worthless the endeavor would be
to have the method just call Gviz?

Thanks for a great package (and a great comparison with CuffLinks in your
paper-to-be),

--t



On Wed, Jun 20, 2012 at 7:45 AM, Elena Sorokin <sorokin@wisc.edu> wrote:

> Hi Alejandro,
> Yes, the merged genes I find are difficult to interpret - because the
> differential exon usage is probably just differences in total gene
> expression. I still wonder about it, because in my mapping procedure, I do
> a very stringent alignment where reads that map to more than one place in
> the transcriptome get thrown out of the BAM file. However, I would say this
> only affects less than 1 in 10 of my differential exon results, so I
> believe I can work around it. I did use the plot function, and it's very
> helpful.
> Thanks and best wishes,
> Elena
>
>
> On 6/19/2012 3:29 AM, Alejandro Reyes wrote:
>
>> Dear Elena,
>>
>> Thanks for your email! The reason that multiple genes are merged into a
>> single one is because they share exons, and it is not obvious to assign
>> this exon to a single gene.  You can see more in detail if you do a
>> "plotDEXSeq" displaying the transcripts.  So far, I have not seen a big
>> problem on it but I can imagine a situation in which the merged genes are
>> differentially expressed: there would be differences in exon usage that are
>> differential expression in reality...
>>
>> Is it introducing messy results for you?
>>
>> Alejandro
>>
>>
>>  Hello,
>>>
>>> How should we be interpreting output from DEXSeq in which some geneIDs
>>> within the DEU results table are denoted by multiple genes separated by +
>>> signs? I can send examples of what I mean to the developers, if my question
>>> is unclear.
>>>
>>> Especially when the architecture of the two or even three genes is quite
>>> different, this  type of output perplexes me. Sorry if my post was answered
>>> elsewhere!
>>>
>>> Best wishes,
>>> Elena
>>>
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>>
>>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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