[BioC] normexp errors

[M Perez]

Thanks Gordon for all your answers.

I am afraid I have more questions, now about “normexp”
background correction, I am trying to use "normexp"
with Limma 1.8 and I got this error 

> RG <- backgroundCorrect(RG, method="normexp",
offset=100);
Corrected array 1 
Corrected array 2 
Error in optim(theta, m2loglik.normexp, control =
list(trace = trace),  : 
  Function cannot be evaluated at initial parameters

Note that only the two first files are corrected for
background the third file seem to have something
wrong, but when I try with Limma 1.96 and I got this
new error: 

>RG <- backgroundCorrect(RG, method="normexp",
offset=100);
Corrected array 1 
Error in optim(c(beta, log(sigma), log(alpha)),
sumloglik, gr = grsumloglik,  : 
        initial value in 'vmmin' is not finite

Now just only the first file could be corrected using
"normexp", I think this problem show up because of the
nature of my files that they are “ScanArray” format
files, as I read in other posts “normexp”  works most
of the time but not on 
all data sets but I would like to know if is possible
to do something before to try the “half” correction.
Any idea what could be the reason of these errors? 
Thank you in advance.
Manuel


--- Gordon K Smyth <smyth at wehi.EDU.AU> escribió:
> 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
> 
> 
> 


		
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