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 >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]