Hi, 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 library(limma) targets_e1a <- readTargets() RG_e1a <-read.maimages(targets_e1a$FileName, columns=list(R="CH2I_MEDIAN", G="CH1I_MEDIAN",Rb="CH2B_MEDIAN",Gb="CH1B_MEDIAN"), annotation=c("NAME","Orfname","SECTOR","SECTORROW","SECTORCOL")) names(RG_e1a$genes) <- c("ID", "Orfname", "Block", "Row", "Column") RG_e1a$printer <- getLayout(RG_e1a$genes, guessdups=TRUE) Thank you so much already, Vanessa -- ================================================================== 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