[BioC] "M vs. M" Plot

[Sean Davis]

On 6/1/06 1:25 PM, "Heather Nyce" <hlg23 at drexel.edu> wrote:

> Hello Bioconductors-
> 
> My apologies for the basic nature of this question.
> 
> In reviewing the archives on dye bias, it was mentioned (Nov. 2005)
> that the simplest way to detect dye effects is to plot M vs. M for the
> dye-swapped arrays.  I have not been able to locate a command line for
> plotting "M vs. M" in limma and am wondering if anyone could
> point me in the right direction?

There isn't such a function.  If you have an MAList called MA, for example,
you can simply do:

 plot(MA$M[,1],MA$M[,2])

To plot the first array versus the second, for example.

Sean