Fwd: Re: [BioC] 2x3 ANOVA

Denise Scholtens dscholtens at northwestern.edu
Thu Jul 15 20:18:21 CEST 2004

>Date: Thu, 15 Jul 2004 12:51:43 -0500
>To: "Jeff Lande" <land0038 at umn.edu>
>From: Denise Scholtens <dscholtens at 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 
>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 -
>>Jeff Lande
>>Graduate Student - University of Minnesota
>>         [[alternative HTML version deleted]]
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>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 at 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 at northwestern.edu

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