[BioC] getting normexp (and log2 transformed) values - not further-processed M values

[Sean Davis]

On Sun, Oct 4, 2009 at 9:20 PM,  <adoty at umd.edu> wrote:
>
> Dear Listserv,
>
> I have an unusual microarray data set -a RIP-ChIP data set- and would like to use the "normexp" function (as found in limma) to background-subtract my data (and I'll take it's log2 data transformation, too) - but I don't want the automatic M and A value output that you can get from limmaGUI.  [This is solely because my data are not the least bit normal and I cannot use limma to analyze them further.]
>
> Is there a way for me to obtain the normexp (and transformed) data from within R?  Is is an "object" that I can "print" or "write" before it gets converted to M values?
>

Hi, Alana.  Have a look at the help for the backgroundCorrect()
function in the limma package.

Sean