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