[BioC] limma printer layout

Gordon Smyth smyth at wehi.EDU.AU
Sun Sep 9 03:18:27 CEST 2007

Dear Vanessa,

limma always assumes complete print-tip-groups, so the only way to 
use imageplot() correctly is to complete your arrays by putting back 
to last 4 spots of each print-tip-group as NA. You can do this by:

   narrays <- ncol(RG_e1)
   Y <- matrix(NA,21632,narrays)
   RG <- new("RGList",list(R=Y,G=Y,Rb=Y,Gb=Y)
   RG$printer <- RG_e1$printer
   missingspots <- spotr(RG$printer)==26 & spotc(RG$printer)>=23
   RG$R[!i,] <- RG_e1$R
   RG$Rb[!i,] <- RG_e1$Rb
   RG$G[!i,] <- RG_e1$G
   RG$Gb[!i,] <- RG_e1$Gb

Best wishes

>Date: Fri, 07 Sep 2007 14:12:45 +0200
>From: Vanessa Vermeirssen <vanessa.vermeirssen at psb.ugent.be>
>Subject: [BioC] limma printer layout
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <46E1403D.6090805 at psb.ugent.be>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>I am trying to read in cDNA spotted microarray data into limma.
>I would like to check for spatial heterogeneity in the samples and
>therefore I would like to define the printer layout.
>I have done this now using a dataframe containing the gene list and
>columns for block, row and column of the array.
>Through getLayout, I get correctly the 4 by 8,26 by 26 dimensions (21632
>spots). However I noticed from the raw data that
>in every block at row 26, 4 columns are skipped, so 4 spots are skipped.
>Therefore in my datafile I only have 21504 spots.
>When I try to check for spatial heterogeneity by:
>  > imageplot(log2(RG_e1a$Gb[,1]),RG_e1a$printer)
>Error in imageplot(log2(RG_e1a$Gb[, 1]), RG_e1a$printer) :
>         Number of image spots does not agree with layout dimensions
>I get this error...
>Is there a way to more precisely define my printer-layout or a way to
>get around this and look at spatial heterogeneity anyway?
>I now copy my code completely, so you have an idea of what I have read
>in already.
>#reading cDNA spotted arrays in Limma Bioconductor package
>targets_e1a <- readTargets()
>RG_e1a <-read.maimages(targets_e1a$FileName,
>names(RG_e1a$genes) <- c("ID", "Orfname", "Block", "Row", "Column")
>RG_e1a$printer <- getLayout(RG_e1a$genes, guessdups=TRUE)
>Thank you so much already,
>Vanessa Vermeirssen, PhD
>Tel:+32 (0)9 331 38 23                        fax:+32 (0)9 3313809
>VIB Department of Plant Systems Biology, Ghent University
>Technologiepark 927, 9052 Gent, BELGIUM
>vamei at psb.ugent.be                         http://www.psb.ugent.be

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