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 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >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 >