[BioC] Surrogate variable analysis (SVA) with Limma

[Augusto Rendon]

Hello,

I have a data set of micro-array experiments (single color illumina)
that is strongly confounded by pedigree relationships. I am just
interested in comparing patients and controls. I would like to give Leek
and Storey's sva algorithm a go with limma, to help deal with
confounding factors. 

Does anybody have some experience doing this?

My main concern is that the sva algorithm assumes a linear model with an
intercept and I would rather use one without it as it is most natural in
order to simply compare two groups.

Thanks,

augusto