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

Giulio Di Giovanni perimessaggini at hotmail.com
Fri Mar 17 17:54:28 CET 2006

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

Thanks a lot !


>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
>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:
>Is this what you wanted?
>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 
>>limma's MAList, but I'm not able to do it.
>>the only way I found is through marray.
>>I did
>>rawset <- read.maimages(source="genepix", ext="gpr")
>>MAset <- normalizeWithinArrays(rawset, method="none")
>># some images from marray
>>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
>>for MA plots...
>>Thanks in advance,
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>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
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu

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