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
