[BioC] limma printer layout
vanessa.vermeirssen at psb.ugent.be
Fri Sep 7 14:12:45 CEST 2007
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:
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
#reading cDNA spotted arrays in Limma Bioconductor package
targets_e1a <- readTargets()
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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