Hi

I am analysing some microarray data with a large amount of different treatment groups and I was wondering whether there is a method in limma which allows you to do an ANOVA like test which will identify any differences between  treatment groups, instead of doing multiple pairwise comparisons? I would also like to use a method which is able to filter the resultant list of differentially expressed genes by log fold change? Is there such a method and does it make sense to do this?

For your first question, yes, look at section 9.3 of the limma user's guide and the documentation relating to topTable. Basically, if you drop multiple coefficients, you can compare multiple groups; also have a look at A: How to use Limma to analyze differences among group items without doing pairwise.

For your second question, while you can filter the DE list by log-fold change, this is not recommended - see the "Note" in ?topTable. Rather, you should consider testing against a log-fold change threshold with treat.