Dear Bioconductor if I had a 2 way ANOVA to analyse, say gender and treatment, where treatment had 3 or more levels (eg placebo, drug1 and drug2) would there be anu way using the limma output object of obtaining the overall p-value for an effect of treatment (as you'd get from an ANOVA table as an F statistic with 2 df )- or can we only obtain p-values for contrasts eg each drug vs placebo many thanks in advance _________________________________________________________________ Celebrate a decade of Messenger with free winks, emoticons, display pics, and more. http://clk.atdmt.com/UKM/go/157562755/direct/01/ [[alternative HTML version deleted]]

Hi Bernard, bernard north wrote: > Dear Bioconductor > > > > if I had a 2 way ANOVA to analyse, say gender and treatment, where > treatment had 3 or more levels (eg placebo, drug1 and drug2) > > would there be anu way using the limma output object of obtaining the > overall p-value for an effect of treatment (as you'd get from an > ANOVA table as an F statistic with 2 df )- or can we only obtain > p-values for contrasts eg each drug vs placebo Have you read the limma User's Guide? I believe section 8.7 is directly concerned with this issue. Best, Jim > > > > many thanks in advance > > _________________________________________________________________ > Celebrate a decade of Messenger with free winks, emoticons, display > pics, and more. http://clk.atdmt.com/UKM/go/157562755/direct/01/ > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- 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