Hi all, I want to test the hypothesis Cond1-(Cond2+Cond3)/2 =0 in glmFIT, do I need to specify (1,-0.5,-0.5) as the contrast vector in glmFit? Also should I include this contrast in glmLRT as well or it automatically uses the contrast used in the previous step? Will the following commands give me what I want? fit <- glmFit(dgelist_object, design,contrast=c(1,-0.5-,-0.5)) lrt <- glmLRT(fit) Thanks, Al [[alternative HTML version deleted]]

glmFit doesn't take a contrast argument as far as I know. You only specify the contrast in glmLRT. On Mon 10 Dec 2012 06:47:40 PM PST, Alpesh Querer wrote: > Hi all, > > I want to test the hypothesis Cond1-(Cond2+Cond3)/2 =0 in glmFIT, do I need > to specify (1,-0.5,-0.5) as the contrast vector in glmFit? > Also should I include this contrast in glmLRT as well or it automatically > uses the contrast used in the previous step? > Will the following commands give me what I want? > > fit <- glmFit(dgelist_object, design,contrast=c(1,-0.5-,-0.5)) > lrt <- glmLRT(fit) > > Thanks, > Al > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

glmLRT doesn't take a design argument. Just a coef or contrast. I believe the documentation for glmLRT indicates that the contrast takes precedence over the coef. On Mon 10 Dec 2012 07:04:16 PM PST, Alpesh Querer wrote: > Thanks Ryan, > > so lrt <- glmLRT(fit,contrast=c(1,-0.5-,-0.5),design) will override > the default coef and coef is no longer required to be specified? > > Regards, > Al > > On Mon, Dec 10, 2012 at 8:50 PM, Ryan C. Thompson > <rct at="" thompsonclan.org="" <mailto:rct="" at="" thompsonclan.org="">> wrote: > > glmFit doesn't take a contrast argument as far as I know. You only > specify the contrast in glmLRT. > > > On Mon 10 Dec 2012 06:47:40 PM PST, Alpesh Querer wrote: > > Hi all, > > I want to test the hypothesis Cond1-(Cond2+Cond3)/2 =0 in > glmFIT, do I need > to specify (1,-0.5,-0.5) as the contrast vector in glmFit? > Also should I include this contrast in glmLRT as well or it > automatically > uses the contrast used in the previous step? > Will the following commands give me what I want? > > fit <- glmFit(dgelist_object, design,contrast=c(1,-0.5-,-0.__5)) > lrt <- glmLRT(fit) > > Thanks, > Al > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" 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="" gmane.science.biology.informatics.conductor=""> > >

Thanks Ryan, so lrt <- glmLRT(fit,contrast=c(1,-0.5-,-0.5),design) will override the default coef and coef is no longer required to be specified? Regards, Al On Mon, Dec 10, 2012 at 8:50 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote: > glmFit doesn't take a contrast argument as far as I know. You only specify > the contrast in glmLRT. > > > On Mon 10 Dec 2012 06:47:40 PM PST, Alpesh Querer wrote: > >> Hi all, >> >> I want to test the hypothesis Cond1-(Cond2+Cond3)/2 =0 in glmFIT, do I >> need >> to specify (1,-0.5,-0.5) as the contrast vector in glmFit? >> Also should I include this contrast in glmLRT as well or it automatically >> uses the contrast used in the previous step? >> Will the following commands give me what I want? >> >> fit <- glmFit(dgelist_object, design,contrast=c(1,-0.5-,-0.**5)) >> lrt <- glmLRT(fit) >> >> Thanks, >> Al >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> 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.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > [[alternative HTML version deleted]]