[BioC] Gal file and Limma

[M Perez]

Hi list,

I have some questions about using new version of Limma
and/or R.

I have read that the last version of Limma have
changes about reading GAL files. I am working with
several input files coming from ScanArray scanner and
I need to read necessarily a GAL file, I don’t have
problems with the R version showing below  and Limma
1.8

platform i386-pc-mingw32
arch     i386           
os       mingw32        
system   i386, mingw32  
status                  
major    2              
minor    0.1            
year     2004           
month    11             
day      15             
language R    


But When I run the same script(see below) under Limma
v. 1.9.3 and R 2.1.0

I got this error
>files <- dir(pattern="\\.txt");
#
>RG <- read.maimages(files, columns=list(Rf="Ch1
Median",Gf="Ch2 Median",Rb="Ch1 B Median",Gb="Ch2 B
Median")); 
#
> RG$genes <- readGAL();
Error in list.files(path, pattern, all.files,
full.names, recursive) : 
        invalid 'pattern' regular expresion


I need to use the last version of Limma because I also
want to use the "normexp" background correction.

I would like to know how I can solve this problem; any
help will be much appreciated.

I send you as attachment a small GAL file with just
few rows as an example.

Thank you for your help.
Manuel



		
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ATF	1			
1	5			
Type=GenePix ArrayList V1.0				
Block	Row	Column	ID	Name
1	1	1	gi|18150858:20626-20940	putative transcriptional repressor
1	1	2	gi|18150858:20626-20940	putative transcriptional repressor
1	1	3	gi|18150858:c106375-105110	putative mating pair formation protein
1	1	4	gi|18150858:c106375-105110	putative mating pair formation protein
1	1	5	DMSO	Control_0
1	1	6	DMSO	Control_0
1	1	7	DMSO	Control_0
1	1	8	DMSO	Control_0
1	1	9	gi|18150858:22773-23357	putative transcriptional regulator protein
1	1	10	gi|18150858:22773-23357	putative transcriptional regulator protein
1	1	11	gi|18150858:c109096-108704	hypothetical protein
1	1	12	gi|18150858:c109096-108704	hypothetical protein
1	1	13	DMSO	Control_0
1	1	14	DMSO	Control_0
1	1	15	DMSO	Control_0
1	1	16	DMSO	Control_0
1	2	1	gi|18150858:16158-16379	hypothetical protein
1	2	2	gi|18150858:16158-16379	hypothetical protein
1	2	3	gi|18150858:96571-96954	putative TraA protein
1	2	4	gi|18150858:96571-96954	putative TraA protein
1	2	5	DMSO	Control_0
1	2	6	DMSO	Control_0
1	2	7	DMSO	Control_0
1	2	8	DMSO	Control_0