Hi All,

I'm unsure where to start with an Analysis. We have Affymetrix data (Clariom S) from an RCT (2 treatment groups, 2 time points) and are wanting to perform a 2-way Repeated Measures ANOVA. Does anyone know if this is possible and which package can do this? I've looked through the Limma package manual haven't had any luck finding anything yet.

Regards,

Evan

limma can fit any linear model, which means it can handle any anova setup including repeated measures. The experiment considered in Section 9.7 of the limma User's Guide is a two-way repeated measures design with two groups and two tissues per individual. That sounds very similar to your experiment (with disease groups instead of treatments and tissues instead of time points).