[BioC] Lumi package - MA plots

[Martin Morgan]

Hi Simone --

I've found it convenient to take the M and A matrices and 'flatten'
them into a data frame, along the lines of

> M <- matrix(rnorm(10000), ncol=5)
> A <- matrix(rnorm(10000), ncol=5)
> colnames(M) <- colnames(A) <- LETTERS[1:5]

> df <- data.frame(Samp=rep(colnames(M), each=nrow(M)),
>                  M=as.vector(M),
>                  A=as.vector(A))

and then use lattice to display the results

> library(lattice)
> xyplot(M~A|Samp, df)

> library(geneplotter)
> xyplot(M~A|Samp, df, panel=panel.smoothScatter)
> xyplot(M~A|Samp, df, panel=function(...) {
>     panel.smoothScatter(...)
>     panel.abline(0,0)
> })

Martin


"Simone de Jong" <s.dejong-6 at umcutrecht.nl> writes:

> I am using the Lumi package to analyze my Illumina expression data (mouse). 
>
> I was wondering whether there is a user friendly way to construct an
> aggregate sample to plot my samples against in MA plots, instead of plotting
> them in a pairwise manner. 
>
>  
>
> Thanks,
>
>  
>
> Simone de Jong, Msc.
>
> PhD student
>
>  
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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