[BioC] limma printer layout

[Vanessa Vermeirssen]

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