>Date: Thu, 15 Jul 2004 12:51:43 -0500 >To: "Jeff Lande" <land0038@umn.edu> >From: Denise Scholtens <dscholtens@northwestern.edu> >Subject: Re: [BioC] 2x3 ANOVA > >> >> >>Now, I'd like to start running some contrasts to see the effects at >>particular graft type/day combinations (ie 14 day allografts) and also >>look at fold changes. I think both of these functions are possible >>within the factDesign package, but I'm not sure how to input the second >>and the third parameters in the par2lambda function. If there's anyone >>who can give me some direction on this, I would greatly appreciate it. > >Hi Jeff, > >par2lambda takes three coefficients - "betaNames", "betas", and "coefs". > >"betaNames" refers to the names of the coefficients that are returned with >the lm, for example, you could do: > >betaNames <- names(lm.full[["coef"]]) > >"betas" and "coefs" are used to define the specific contrasts of >interest. The idea of the par2lambda function is not to have to construct >a contrast matrix by hand - if you did have to do this, you would need to >look at the order of the coefficients returned by the lm and make sure >your contrast matrix is specified accordingly. When performing many >contrasts on several different factors, this can be a pain. In any event, >suppose your lm returns coefficients named "beta1", "beta2", "beta3", and >"beta4" and you want to test the contrast beta2 - beta4=0. Then you would >specify > >betas <- list(c("beta2","beta4")) >coefs <- list(c(1,-1)) > >and you're all set to use the par2lambda function. The list structure is >helpful if you want to simultaneously test two or more contrasts. Suppose >in addition to beta2-beta4=0, you want to test beta3+beta4=0. Then you >would say > >betas <- list(c("beta2","beta4"),c("beta3","beta4")) >coefs <- list(c(1,-1),c(1,1)) > >par2lambda(betaNames,betas,coefs) will then return the appropriate >contrast matrix for use with contrastTest or findFC. There are examples >of how to specify these parameters in the documentation example for the >par2lambda function and also in the factDesign vignette. > >Hope this helps - >Denise > > > >> >>Thanks, >> >>Jeff Lande >>Graduate Student - University of Minnesota >> >> >> [[alternative HTML version deleted]] >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >****************************************** >Denise Scholtens, Ph.D. >Research Assistant Professor >Northwestern Medical School >Department of Preventive Medicine >680 N. Lake Shore Drive Suite 1102 >Chicago, IL 60614 >phone: 312.503.7261 >fax: 312.908.9588 >dscholtens@northwestern.edu ****************************************** Denise Scholtens, Ph.D. Research Assistant Professor Northwestern Medical School Department of Preventive Medicine 680 N. Lake Shore Drive Suite 1102 Chicago, IL 60614 phone: 312.503.7261 fax: 312.908.9588 dscholtens@northwestern.edu

Thanks Denise, My initial setup was reading Gday as a covariate rather than a factor. I changed the values of 4, 14 and 25 to "4d", "14d" and "25d" and with the resulting coefficients, it makes a lot more sense. Jeff > -----Original Message----- > From: Denise Scholtens [mailto:dscholtens@northwestern.edu] > Sent: Thursday, July 15, 2004 1:18 PM > To: bioconductor@stat.math.ethz.ch; land0038@umn.edu > Subject: Fwd: Re: [BioC] 2x3 ANOVA > > > >Date: Thu, 15 Jul 2004 12:51:43 -0500 > >To: "Jeff Lande" <land0038@umn.edu> > >From: Denise Scholtens <dscholtens@northwestern.edu> > >Subject: Re: [BioC] 2x3 ANOVA > > > >> > >> > >>Now, I'd like to start running some contrasts to see the effects at > >>particular graft type/day combinations (ie 14 day allografts) and also > >>look at fold changes. I think both of these functions are possible > >>within the factDesign package, but I'm not sure how to input the second > >>and the third parameters in the par2lambda function. If there's anyone > >>who can give me some direction on this, I would greatly appreciate it. > > > >Hi Jeff, > > > >par2lambda takes three coefficients - "betaNames", "betas", and "coefs". > > > >"betaNames" refers to the names of the coefficients that are returned > with > >the lm, for example, you could do: > > > >betaNames <- names(lm.full[["coef"]]) > > > >"betas" and "coefs" are used to define the specific contrasts of > >interest. The idea of the par2lambda function is not to have to > construct > >a contrast matrix by hand - if you did have to do this, you would need > to > >look at the order of the coefficients returned by the lm and make sure > >your contrast matrix is specified accordingly. When performing many > >contrasts on several different factors, this can be a pain. In any > event, > >suppose your lm returns coefficients named "beta1", "beta2", "beta3", and > >"beta4" and you want to test the contrast beta2 - beta4=0. Then you > would > >specify > > > >betas <- list(c("beta2","beta4")) > >coefs <- list(c(1,-1)) > > > >and you're all set to use the par2lambda function. The list structure is > >helpful if you want to simultaneously test two or more contrasts. > Suppose > >in addition to beta2-beta4=0, you want to test beta3+beta4=0. Then you > >would say > > > >betas <- list(c("beta2","beta4"),c("beta3","beta4")) > >coefs <- list(c(1,-1),c(1,1)) > > > >par2lambda(betaNames,betas,coefs) will then return the appropriate > >contrast matrix for use with contrastTest or findFC. There are examples > >of how to specify these parameters in the documentation example for the > >par2lambda function and also in the factDesign vignette. > > > >Hope this helps - > >Denise > > > > > > > >> > >>Thanks, > >> > >>Jeff Lande > >>Graduate Student - University of Minnesota > >> > >> > >> [[alternative HTML version deleted]] > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor@stat.math.ethz.ch > >>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >****************************************** > >Denise Scholtens, Ph.D. > >Research Assistant Professor > >Northwestern Medical School > >Department of Preventive Medicine > >680 N. Lake Shore Drive Suite 1102 > >Chicago, IL 60614 > >phone: 312.503.7261 > >fax: 312.908.9588 > >dscholtens@northwestern.edu > > ****************************************** > Denise Scholtens, Ph.D. > Research Assistant Professor > Northwestern Medical School > Department of Preventive Medicine > 680 N. Lake Shore Drive Suite 1102 > Chicago, IL 60614 > phone: 312.503.7261 > fax: 312.908.9588 > dscholtens@northwestern.edu