[BioC] Gal file and Limma

[Gordon K Smyth]

This problem is caused by a new "feature" of R 2.1.0, stricter regular expression syntax.  It has
been fixed in limma 1.9.5.

Gordon

> Date: Thu, 19 May 2005 11:44:23 +0200 (CEST)
> From: M Perez <perezperezmm at yahoo.es>
> Subject: [BioC] Gal file and Limma
> To: bioconductor at stat.math.ethz.ch
>
> 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
>
>
>
>
> ______________________________________________
>
> Nuevos servicios, más seguridad
> -------------- next part --------------
> 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