[BioC] limma: percent of variance explained

[Julien Roux]

Dear all,
I am analyzing an RNA-seq experiment with voom+limma.
The design of the experiment had two fixed effect factors that I 
combined into one vector including all combinations of the levels of the 
2 factors (as explained in the limma user guide, section 9.5), and a 
random effect that I model using the block and correlation arguments in 
lmFit.
I am wondering if it would be possible to estimate, for each gene, what 
is the proportion of variance explained by each factor from the lmFit 
result? Is it possible to get ANOVA-like tables for all genes? Is it 
also possible to get the proportion of variance explained by the random 
effect factor?
I have seen this kind of analysis performed in published studies (e.g., 
Figure 3c in t Hoen PA et al. 2013 Nat Biotechnol 
http://www.ncbi.nlm.nih.gov/pubmed/24037425), but the details are 
missing in the Materials & Methods.
Thanks a lot for your help
Julien

-- 
Julien Roux, PhD
Gilad lab, Department of Human Genetics, University of Chicago
http://giladlab.uchicago.edu/
920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
tel: +1-773-834-1984   fax: +1-773-834-8470