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Piotr Stępniak
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90
@piotr-stepniak-2827
Last seen 10.3 years ago
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 St?pniak