[BioC] "M vs. M" Plot

Sean Davis sdavis2 at mail.nih.gov
Thu Jun 1 20:30:54 CEST 2006

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:


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


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