[BioC] Obtaining Normalised Signal intensities

[Sean Davis]

On Fri, May 7, 2010 at 12:04 PM, Lloyd, Bryony
<Bryony.Lloyd at liverpool.ac.uk> wrote:
> Hi,
>
> I was hoping that someone might be able to help me. I have inherited data from 4 Agilent arrays. I would like to recover and output to file the normalised signal intensity of the Cy3 and Cy5 data if possible, rather than  the log ratio of each. If anyone can suggest a way to do this I would be most grateful.
> As the MA can be use by plotDensities() to show the effect of normalisation upon signal intensities, I'm hoping that this will be possible.
> Hope you can help.

See the RG.MA in limma, assuming that you have an MAList.  If not,
you'll need to be more specific about what you have.

Sean