[BioC] How to boxplot Print tip group intensities with limma, out from marra

[Giulio Di Giovanni]

Gosh ! It was the only thing I didn't look at !

Thanks a lot !

Giulio



>From: Jenny Drnevich <drnevich at uiuc.edu>
>To: "Giulio Di Giovanni" <perimessaggini at hotmail.com>,        
>bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] How to boxplot Print tip group intensities with  limma, 
>out from marray objects ?
>Date: Fri, 17 Mar 2006 10:44:47 -0600
>
>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
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu
>