Begin forwarded message: > From: Michael Muratet <mmuratet at="" hudsonalpha.org=""> > Date: October 24, 2011 2:21:22 PM CDT > To: bioconductor at r-project.org > Subject: F values from topTable with coef=NULL testing all zero or > all equal? > > 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? > Hello again I just realized that the test is on log differential expression, and rejecting the null hypothesis values equal to zero implies differential expression. Cheers Mike > 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 > > > > > 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