[BioC] MA plots for large number of arrays
Martin Morgan
mtmorgan at fhcrc.org
Thu Nov 3 13:20:06 CET 2011
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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