Question: interpreting DEXSeq output
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gravatar for Elena Sorokin
7.3 years ago by
Elena Sorokin150
Elena Sorokin150 wrote:
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
dexseq • 1.3k views
ADD COMMENTlink modified 7.3 years ago by Alejandro Reyes1.7k • written 7.3 years ago by Elena Sorokin150
Answer: interpreting DEXSeq output
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gravatar for Alejandro Reyes
7.3 years ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.3 years ago by Alejandro Reyes1.7k
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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 7.3 years ago by Elena Sorokin150
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]]
ADD REPLYlink written 7.3 years ago by Tim Triche4.2k
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