Doubt on time course design

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I'm writing because I have a doubt on how to perform a DGE analysis with edgeR. I followed both the tutorial and some interenet posts, but I got confused and I'm not sure on how to properly account for variation between individuals in my experimental design that is the following: RNA-Seq data of 6 subjects at 4 different time points (24 obs). There is no control/treatment. My goal is to reveal genes that are differentially expressed between the time points. Should I design the matrix as follows? designMatrix <- model.matrix(~subjects+timepoints) Or there is something that I misinterpret? Any advices on this issue? Thank you all for your cooperation. -- output of sessionInfo(): ... -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 11.5 years ago by Aliaksei Holik ▴ 350 • written 11.5 years ago by Guest User ★ 13k

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Aliaksei Holik ▴ 350

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Dear Stephano, Unless you are looking for differential gene expression between subjects my suggestion would be: designMatrix <- model.matrix(~timepoints) OR designMatrix <- model.matrix(~0+timepoints) Depending on whether or not you wish to include the intercept term. Hope it helps, Aliaksei. On 19/07/2013 20:01, Stefano Capomaccio [guest] wrote: > > I'm writing because I have a doubt on how to perform a DGE analysis with edgeR. > I followed both the tutorial and some interenet posts, but I got confused and I'm not sure on how to properly account for variation between individuals in my experimental design that is the following: > > RNA-Seq data of 6 subjects at 4 different time points (24 obs). There is no control/treatment. > My goal is to reveal genes that are differentially expressed between the time points. > > Should I design the matrix as follows? > > designMatrix <- model.matrix(~subjects+timepoints) > > Or there is something that I misinterpret? > Any advices on this issue? > > Thank you all for your cooperation. > > -- output of sessionInfo(): > > ... > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 COMMENT • link 11.5 years ago Aliaksei Holik ▴ 350

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Oops. Too quick off the mark there. After replying I realised that you'd want to block the subject variable. And in that case your design matrix seems correct. Sorry for replying without thinking :) On 19/07/2013 23:13, Aliaksei Holik wrote: > Dear Stephano, > > Unless you are looking for differential gene expression between subjects > my suggestion would be: > > designMatrix <- model.matrix(~timepoints) > > OR > > designMatrix <- model.matrix(~0+timepoints) > > Depending on whether or not you wish to include the intercept term. > > Hope it helps, > > Aliaksei. > > On 19/07/2013 20:01, Stefano Capomaccio [guest] wrote: >> >> I'm writing because I have a doubt on how to perform a DGE analysis >> with edgeR. >> I followed both the tutorial and some interenet posts, but I got >> confused and I'm not sure on how to properly account for variation >> between individuals in my experimental design that is the following: >> >> RNA-Seq data of 6 subjects at 4 different time points (24 obs). There >> is no control/treatment. >> My goal is to reveal genes that are differentially expressed between >> the time points. >> >> Should I design the matrix as follows? >> >> designMatrix <- model.matrix(~subjects+timepoints) >> >> Or there is something that I misinterpret? >> Any advices on this issue? >> >> Thank you all for your cooperation. >> >> -- output of sessionInfo(): >> >> ... >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 >> >> > > _______________________________________________ > 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 REPLY • link 11.5 years ago Aliaksei Holik ▴ 350

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Dear Aliaksei, thank you for your help! Stefano On Fri, Jul 19, 2013 at 3:28 PM, Aliaksei Holik <salvador@bio.bsu.by> wrote: > Oops. Too quick off the mark there. After replying I realised that you'd > want to block the subject variable. And in that case your design matrix > seems correct. > > Sorry for replying without thinking :) > > > On 19/07/2013 23:13, Aliaksei Holik wrote: > >> Dear Stephano, >> >> Unless you are looking for differential gene expression between subjects >> my suggestion would be: >> >> designMatrix <- model.matrix(~timepoints) >> >> OR >> >> designMatrix <- model.matrix(~0+timepoints) >> >> Depending on whether or not you wish to include the intercept term. >> >> Hope it helps, >> >> Aliaksei. >> >> On 19/07/2013 20:01, Stefano Capomaccio [guest] wrote: >> >>> >>> I'm writing because I have a doubt on how to perform a DGE analysis >>> with edgeR. >>> I followed both the tutorial and some interenet posts, but I got >>> confused and I'm not sure on how to properly account for variation >>> between individuals in my experimental design that is the following: >>> >>> RNA-Seq data of 6 subjects at 4 different time points (24 obs). There >>> is no control/treatment. >>> My goal is to reveal genes that are differentially expressed between >>> the time points. >>> >>> Should I design the matrix as follows? >>> >>> designMatrix <- model.matrix(~subjects+**timepoints) >>> >>> Or there is something that I misinterpret? >>> Any advices on this issue? >>> >>> Thank you all for your cooperation. >>> >>> -- output of sessionInfo(): >>> >>> ... >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> ______________________________**_________________ >>> 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.**conduc tor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> >>> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.**conduct or<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >> >> >> -- .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. *He tried to be a scientist* Stefano Capomaccio, PhD Università Cattolica del Sacro Cuore Via Emilia Parmense, 84 29122 - Piacenza (PC), Italy Phone +39 0523 599203 (office) Phone +39 0523 599482 (lab) email: stefano.capomaccio@unicatt.it email: capemaster@gmail.com skype: capemaster .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. [[alternative HTML version deleted]]

ADD REPLY • link 11.5 years ago Stefano Capomaccio ▴ 10

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