[BioC] limma - MA

Jenny Drnevich drnevich at uiuc.edu
Thu Dec 21 16:56:29 CET 2006

Hi João,

As Hans-Ulrich said, the default value of plotMA is to not plot spots with 
weight = 0. However, if you want to keep your flags set at weight=0.1, but 
not plot them, you just weren't subsetting the RG$weights correctly; to 
plot array 1, you have to subset the RG$weights for array/column 1:

plotMA(RG[(RG$weights[,1])>0.1,], array=1)


At 01:22 AM 12/21/2006, João Fadista wrote:
>Content-Disposition: inline
>Content-Type: text/plain
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>Dear all,
>I am not able to plot only the MA values for the spots with no flags. Here 
>is my code and the error:
>RG <- read.maimages(fnames, source="genepix", path=datadir, ext="gpr", 
>columns=columns, wt.fun=wtflags(0.1))
>RG$printer <- getLayout(RG$genes,guessdups=TRUE)
>types <- readSpotTypes("SpotTypes.txt",path=genedir)
>RG$genes$Status <- controlStatus(types, RG)
> > plotMA(RG[(RG$weights)>0.1,], array=1)
>Error in `[.RGList`(RG, (RG$weights) > 0.1, ) :
>         (subscript) logical subscript too long
>Does anybody know how to do it?
>Best regards
>João Fadista
>Ph.d. student
>         Danish Institute of Agricultural Sciences
>Research Centre Foulum
>Dept. of Genetics and Biotechnology
>Blichers Allé 20, P.O. BOX 50
>DK-8830 Tjele
>Phone:  +45 8999 1900
>Direct: +45 8999 8999
>E-mail: Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk>
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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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