[BioC] Question about F test in limma

[Lisa Mijung Chung]

Thank you very much, all limma experts,  that is a big help to me.

Lisa

On Mon, Apr 28, 2008 at 11:44 AM, Claus-Dieter Mayer <claus at bioss.ac.uk> wrote:
> Dear Lisa,
>
>  no this is not a chance finding. Whether you  include all 3 possible
> contrasts or just the two you specify below: if all contrasts are zero this
> is equivalent to the overall null hypothesis that all 3 treatment means are
> the same, i.e. the F-test is testing the same hypothesis in both cases and
> thus gives the same p-value.
>
>  Best Wishes
>
>  Claus
>
>
>
>  Lisa Mijung Chung wrote:
>
> > Dear limma expert,
> >
> > Thank you very much for your prompt reply. After I had sent you
> > previous email, I tried with both methods just for my curiosity and
> > got the same result. I am wondering if it happens to my data by chance
> > or limma calculates moderated F stat by considering all targets
> > specified on contrast matrix as different treatment groups, i.e. all
> > RNA1, RNA2, and RNA3 appear on (anyways)
> >
> >
> > > makeContrasts(RNA2-RNA1, RNA3-RNA2)
> > >
> > >
> > Thanks, again,
> >
> > Sincerely,
> > Lisa C.
> >
> >
> > On Wed, Apr 23, 2008 at 9:13 PM, Dejian Zhao <zhaodj at ioz.ac.cn> wrote:
> >
> >
> > > I think you should make all pairwise comparisons.
> > >  Your H0 (no difference) means that all the targets show no
> > >  difference. Therefore you should check them pairwise thoroughly.
> > >
> > >
> > >
> > >  On Thu, Apr 24, 2008 09:26, Lisa Mijung Chung wrote:
> > >  > Dear limma expert,
> > >  > I have a question about performing F-test (with several groups) on
> > >  > limma.
> > >  > If I have 3 targets (using Affy chips) called RNA1, RNA2, RNA3 and
> > >  > want to get F statistic to test
> > >  > H0: no difference vs. H1: at least one target is different,
> > >  > (Similar with example on Section 8.6 of limma user guide at
> > >  > pp.42-43)
> > >  >
> > >  > Should I construct my contrast matrix:
> > >  >> makeContrasts(RNA2-RNA1, RNA3-RNA2, RNA3-RNA1) # with all pairwise
> > >  >> comparisons
> > >  >
> > >  > or would it be fine only with:
> > >  >> makeContrasts(RNA2-RNA1, RNA3-RNA2)            # comparisons of
> > >  >> two adjacent pairs
> > >  >
> > >  > With best wishes,
> > >  > Thank you.
> > >  >
> > >  >
> > >  > --
> > >  > Lisa Mijung Chung
> > >  > Graduate Student, Biostat Trainee
> > >  > Department of Statistics, UW-Madison
> > >  > Web: www.stat.wisc.edu/~lchung
> > >  >
> > >  > _______________________________________________
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> > >  > Search the archives:
> > >  > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >  >
> > >
> > >
> > >  --
> > >  De-Jian Zhao
> > >  Institute of Zoology,Chinese Academy of Sciences
> > >  +86-10-64807217
> > >  zhaodj at ioz.ac.cn
> > >
> > >
> > >
> >
> >
> >
> >
> >
>
>  --
>
> ***********************************************************************************
>  Dr Claus-D. Mayer                    | http://www.bioss.ac.uk
>  Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
>  Rowett Research Institute            | Telephone: +44 (0) 1224 716652
>  Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349
>
> ***********************************************************************************
>
>
>



-- 
Lisa Mijung Chung
Graduate Student, Biostat Trainee
Department of Statistics, UW-Madison
Web: www.stat.wisc.edu/~lchung