[BioC] How to boxplot Print tip group intensities with limma, out from marray objects ?

[Jenny Drnevich]

Hi,

I had been wanting to figure out this as well, and your questions prompted 
me to finally do it. Turns out it was pretty simple, if you have a column 
of "block" information == print tip:

boxplot(MAset$M[,1]~MAset$genes$Block)

Is this what you wanted?

Cheers,
Jenny

At 10:22 AM 3/17/2006, Giulio Di Giovanni wrote:
>Hi guys,
>
>I was trying to have a boxplot of M values by print-tip group starting from
>limma's MAList, but I'm not able to do it.
>
>the only way I found is through marray.
>
>I did
>
>library(limma)
>rawset <- read.maimages(source="genepix", ext="gpr")
>MAset <- normalizeWithinArrays(rawset, method="none")
>
># some images from marray
>
>library(convert)
>rawmarray <- as(rawset, "marrayRaw")
>boxplot(rawmarray[,1], xvar = "maPrintTip", yvar = "maM")
>
>
>and this it works perfectly. But I would like to have a clean script,
>without recurring to marray.. And  it's also to learn how to do it...
>
>Do someone knows if it is possible, and how to do it ? I guess it is, as
>limma have
>
>plotPrintTipLoess()
>
>for MA plots...
>
>Thanks in advance,
>
>Giulio
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu