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 at 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.