On Oct 25, 2011, at 8:11 AM, James W. MacDonald wrote: > Hi Michael, > > On 10/24/2011 3:21 PM, Michael Muratet wrote: >> Greetings >> >> This has probably been answered before, but I can't narrow the >> search down enough to find it in the archives. I am looking at the >> output from and documentation for eBayes and realized that the null >> hypothesis for the F statistic is that all the expression values >> are zero. I want to test the hypothesis that all the expression >> values are equal, i.e., rejection implies differential expression. >> I see from the topTable documentation that calling it with >> coef=NULL will yield an F statistic calculation, and I infer from >> the docs it will include all the conditions. What is the null >> hypothesis: that all the values are equal, or that all the values >> are zero? > > I think you misunderstood the help for eBayes(). It states that the > F-statistic tests that all _contrasts_ are zero, which is not the > same as all expression values equal to zero (which wouldn't make > sense). > > If a contrast is equal to zero, it implies no differential > expression between the samples compared in that contrast (or more > correctly, a sufficiently small F-statistic implies that you are > unable to reject the null hypothesis of a difference in any > contrast). Note that you are only testing those contrasts that you > specified via a contrasts matrix, or specified indirectly via your > design matrix. > > Best, > > Jim Thanks, I understand it now. M > > >> >> Thanks >> >> Mike >> >> >> >> Michael Muratet, Ph.D. >> Senior Scientist >> HudsonAlpha Institute for Biotechnology >> mmuratet at hudsonalpha.org >> (256) 327-0473 (p) >> (256) 327-0966 (f) >> >> Room 4005 >> 601 Genome Way >> Huntsville, Alabama 35806 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806