[BioC] DESeq and contrasts

[wang peter]

On Fri, Jul 13, 2012 at 11:54 AM, wang peter <wng.peter at gmail.com> wrote:
> for your question
> fit0 <- fitNbinomGLMs(CDS,count~1)
> fit1 <- fitNbinomGLMs(CDS,count~treatment)
> fit2 <- fitNbinomGLMs(CDS,count~genotype)
> fit3 <- fitNbinomGLMs(CDS,count~treatment+genotype)
> fit4 <- fitNbinomGLMs(CDS,count~treatment*genotype)
>
> ### Inference
> #
> # 1. Which genes are affected by treatment?
>
> Pvals_Trt <- nbinomGLMTest(fit3,fit2)
>
> # 2. Which genes are affected by genotype?
> Pvals_Trt <- nbinomGLMTest(fit3,fit1)
>
> i donot think your sample number is enough to test the interaction of
> "treatment" and "genotype"
>
>
> --
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
> Office phone: 1-607-254-1267(day)
> Official email:sg839 at cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253



-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253