Entering edit mode
M PEREZ
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110
@m-perez-1039
Last seen 9.8 years ago
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@wehi.edu.au> escribi?:
> 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@yahoo.es>
> > Subject: [BioC] Gal file and Limma
> > To: bioconductor@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, m?s 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
>
>
>
______________________________________________
Nuevos servicios, m?s seguridad
