[BioC] MA plots for large number of arrays

[Martin Morgan]

On 11/03/2011 04:15 AM, mjonczyk wrote:
> Dear Juliet,
>
> you can also see plotMA3by2 function in limma, it produces pictures
> (jpg, png, pdf)
> with six arrays in each file. This command will print pictures for all
> arrays.

I find lattice to be useful in this context

 > library(lattice)
 > library(ALL)
 > data(ALL)
 > M = exprs(ALL) - exprs(ALL)[,1]
 > A = (exprs(ALL) + exprs(ALL)[,1]) / 2
 > df = data.frame(M=as.vector(M[,-1]), A=as.vector(A[,-1]),
+                 Id=sampleNames(ALL)[col(M[,-1])])
 > xyplot(M~A|Id, df, layout=c(5,5), pch=".")

Martin

>
> Best Wishes,
> Maciej Jończyk
>


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