[BioC] Question about F test in limma

[Lisa Mijung Chung]

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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>  >
>
>
>  --
>  De-Jian Zhao
>  Institute of Zoology,Chinese Academy of Sciences
>  +86-10-64807217
>  zhaodj at ioz.ac.cn
>



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