Hi Max, Max Kauer wrote: > I have a very basic question about limma. > Assume I have experiments from 3 or more RNA sources in a reference > design. It is easy to define individual contrasts but I want to specify a > contrast matrix that tests for significant differences among ALL the > different RNA sources (i.e. the analogous thing to a simple One-Way ANOVA). > How can I do that? > Thanks! > Max
Although limma is available on CRAN, it is primarily a Bioconductor package, so this question is better asked on the BioC listserv. As for your question, a simple one-way ANOVA doesn't test for significant differences between all factor levels - it tests for _any_ difference between factor levels. The only way to test for significant differences among all the factor levels is to construct a contrasts matrix that includes all possible comparisons. You could then use decideTests() with method = "nestedF" and look for those genes that are significant in all contrasts. HTH, Jim > > > -- > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
