[BioC] illumina --> limma?

[Anand Patel]

Using both mouse and human Sentrix-6 beadarrays, I've managed to
normalize the arrays both with the beadarray package and the
BeadExplorer package.  However, despite being able to get an exprSet
from beadarray and a BeadSummaryList from BeadExplorer, I'm not sure
how to go to Limma from there.

The exprSet does contain normalized values for all of the arrays, and
I can construct a new phenoData, but they're not log-values of
expression . . .

>Usage: lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation=0.75,w
>eights=NULL,method="ls",...)
>Arguments: object: object of class 'numeric', 'matrix', 'MAList',
'marrayNorm', 'exprSet' or 'PLMset' >containing log-ratios or
log-values of expression for a series of microarrays

How best to get them from their current status in an exprSet to Log2
for use in Limma?  Looking at this, I suspect it's something easy --
just take the Log base 2 of each value, then run that modified exprSet
through, but am not sure how to do that easily in R.

Thanks,
Anand C. Patel, MD
Washington University School of Medicine
acpatel at gmail.com