[BioC] Implications of design argument to limma::voom?

[Ryan C. Thompson]

Hi,

I'm using limma's voom function to analyze some of my data, and I'm 
wondering about the implications of the design argument to voom. The 
default design is an intercept-only design, i.e. a model formula of ~1. 
However, I can also pass in the same experimental design that I will 
pass to lmFit later (or conceivably any other design). I'm not entirely 
sure what assumptions I'm making by choosing either of these options. 
Can someone familiar with such things explain what the implications of 
passing or not passing a design to voom are?

Similarly, I have the same question for DESeq's 
varianceStabilizingTransformation: I can use estimateDispersions with or 
without a design matrix and then do the VST either way, and I'm not sure 
what assumptions I am making in either case.

Thanks,

-Ryan Thompson