There are multiple mentions of ANOVA and "two way" in the document you
mention, for example section 8.8.  I strongly suggest you speak to a
statistician to review this document with you and give you pointers to
other suitable materials.

On Mon, Mar 26, 2012 at 10:54 AM, konika chawla <chawla@bio.ntnu.no> wrote:

> Hi
> Sorry but if you mean
>
> http://bioconductor.org/packages/2.6/bioc/vignettes/limma/inst/doc/usersguide.pdf
> <
> http://bioconductor.org/packages/2.6/bioc/vignettes/limma/inst/doc/usersguide.pdf
> >
> There is nothing about using anova in this document.
> Could you please point me to another document, which explains ANOVA?
> Thanks
> Konika
>
>
> On 03/26/2012 03:57 PM, James W. MacDonald wrote:
> > Hi Konika,
> >
> > As Sean already mentioned, you might want to look at the limma
> > package. It seems you have not done so, in which case I will also
> > advise you to to do so.
> >
> > In particular, you should look at the limma User's Guide.
> >
> > Best,
> >
> > Jim
> >
> > On 3/23/2012 10:15 AM, konika chawla wrote:
> >> Hi
> >> I tried using the code below for the data design I have
> >> aof<- function(x) {
> >>     m<-data.frame(time, treatmentA, treatmentB, x);
> >>     anova(aov(x ~ time + treatmentA + treatmentB + time * treatmentA *
> >> treatmentB, m))
> >> }
> >> time<- factor(c(1,1,1,2,2,2,1,1,1,2,2,2,1,1,1,2,2,2))
> >>    treatmentA<-factor(c(1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0)) #control
> >> treatmentB<-factor(c(0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1)) #infected
> >> anovaresults<- apply(val, 1, aof)
> >>
> >> could you check if it is the correct way to put factors , based on the
> >> design mentioned previously.
> >> Also, It gives a huge file for each gene and the Fvalues and Pvalues.
> >> Wondering how to write the result in order to get P values for effect of
> >> treatmentB , or for checking if treatment A and B are same of different.
> >> Could you help
> >> Thanks
> >> Konika
> >>
>
>
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>
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