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 > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor at stat.math.ethz.ch > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > 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