[BioC] limma wrongly reading data

[Wolfgang Huber]

Dear Piotr,

thank you for your report. I suppose that unless you supply (some of) 
the .gpr files that cause your problem, and a more precise description 
of what the problem is, it will be difficult to help you.

Also, please use the latest release of R and limma. There will be more 
common interest in discussing these than for obsolete versions.

  Best wishes
	Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

Piotr Stępniak a écrit 01/06/2008 23:33:
> 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