Hi,

I want to test the effect of having three different genotypes as opposed to
having no different genotypes.
I hope this clarifies my question.

Thanks,
Shreyartha

On Tue, Apr 5, 2011 at 4:52 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Tue, Apr 5, 2011 at 5:04 PM, Shreyartha Mukherjee
> <shreyartha@gmail.com> wrote:
> > Hi Gondon,Bioconductor experts,
> >
> > I have RNA-seq data for 3 genotypes(each genotype having 3 biological
> > replicates) and 30,000 genes.
> > I was trying to find out differentially expressed genes across all
> > genotypes. Here is the code I am using.
> >
> >  library(edgeR)
> > y<-read.table('test_12339.txt'
> > )
> >  d <- DGEList(y, group = rep(1:3, each = 3), lib.size = lib.sizes)
> >  d <- calcNormFactors(d)
> >  times <- rep(c("p1","p2","f1"),c(3,3,3))
> >  times <- factor(times,levels=c("p1","p2","f1"))
> >  design <- model.matrix(~factor(times))
> > disp <- d2$tagwise.dispersion
> >  fit <- glmFit(d,design,dispersion=disp)
> >  lrt <- glmLRT(d,fit)
> > topTags(lrt)
> >
> > Does this code provide me with tags differentially expressed across all
> > conditions? (I am not looking for pairwise differential expression
> > but across all conditions)
>
> Out of curiosity, what does it mean for a gene to be differentially
> expressed in all (three) conditions?
>
> I mean -- what would its expression pattern look like across your
> three genotypes?
>
> If G1, G2, and G3 are your three different genotypes, are you looking
> for a gene A that's differentially expressed when you compare G1 vs.
> G2 AND G2 vs G3 AND G1 vs G3 (or something(?))
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>

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