[BioC] limma wrongly reading data

[Piotr Stępniak]

Hello Everyone,

I am having problems using limma to analyse my data. It seems that
when executing the function read.maimages() over the data it gets read
wrongly - the values are taken from first next to right column. So for
example under "F543
Median" I get "F543 Mean" values and so on, this causes printer layout
problem and any other function used on the data to fail...

The function to read data looks like this:
bialkoRaw<- read.maimages( dir(pattern="gpr"), columns=list(G="F543
Median", Gb="B543 Median", R="F633 Median", Rb="B633 Median"),
annotation=c("Block", "Column", "Row", "Name", "ID"), row.names=NULL,
stringsAsFactors = default.stringsAsFactors())

My sessionInfo():

R version 2.6.2 (2008-02-08)
i486-pc-linux-gnu

locale:
C

attached base packages:
 [1] grid      splines   tools     stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] arrayQuality_1.18.0  gridBase_0.4-3       hexbin_1.14.0
 [4] convert_1.16.0       RColorBrewer_1.0-2   cluster_1.11.10
 [7] arrayMagic_1.16.1    genefilter_1.16.0    survival_2.34-1
[10] marray_1.18.0        vsn_3.6.0            affy_1.16.0
[13] preprocessCore_1.0.0 affyio_1.8.0         Biobase_1.16.3
[16] lattice_0.17-7       limma_2.14.1

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.0.6 DBI_0.2-4           RSQLite_0.6-8
[4] annotate_1.18.0     rcompgen_0.1-17     tcltk_2.6.2


Does anyone have any idea what might be wrong?
I'd appreciate any help.

Kind Regards,
Piotr Stępniak