[BioC] SNPRMA: Normalizing...Error in readChar(con, 5) : cannot open the connection

[Alex Lisovich]

Benilton,

Now it's working.
Thank you very much!

Alex

On 6/25/07, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> The pd.mapping packages contain metadata information not available on
> the Affymetrix files.
>
> So, use this instead:
>
> http://www.bioconductor.org/packages/2.0/data/annotation/html/
> pd.mapping250k.sty.html
>
> b
>
> On Jun 25, 2007, at 11:46 AM, Alex Lisovich wrote:
>
> > Benilton,
> >
> > The OS is Mac OSX Tiger on dual-core intel MacPro.
> >
> > The pd.mapping250k.sty was built from Affymetris .cdf, .csv and
> > probe_tab files using pdInfoBuilder and installed through R
> > -arch=x86_64 CMD INSTALL.
> >
> > The sessioInfo() and traceback():
> >
> >> sessionInfo()
> > R version 2.5.0 Patched (2007-05-02 r41420)
> > x86_64-apple-darwin8.9.1
> >
> > locale:
> > C
> >
> > attached base packages:
> > [1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
> > "utils"
> > [7] "datasets"  "methods"   "base"
> >
> > other attached packages:
> >   pd.mapping250k.sty                 oligo BufferedMatrixMethods
> >              "0.1.5"             "1.0.2-6"               "1.0.0"
> >       BufferedMatrix               RSQLite                   DBI
> >              "1.0.0"               "0.5-4"               "0.2-3"
> >               affyio               Biobase
> >              "1.4.0"              "1.14.0"
> >>
> >
> >> traceback()
> > 3: readChar(con, 5)
> > 2: load(system.file("extdata", paste(annot, "Ref.rda", sep = ""),
> >       package = annot))
> > 1: snprma(rawData)
> >>
> >
> > Thank you,
> >
> > Alex
> >
> > On 6/23/07, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> >> What are your sessionInfo() and traceback()?
> >>
> >> If you installed the pd.mapping pkgs from the source, make sure
> >> you're using the latest version.
> >>
> >> If your OS is windows, we're working on a solution for the pd.mapping
> >> pkgs.
> >>
> >> b
> >>
> >> On Jun 23, 2007, at 10:56 AM, Alex Lisovich wrote:
> >>
> >> > Dear All,
> >> >
> >> > I am getting the following error when using snprma() on oligo
> >> > v.1.0.2-6 with pd.mapping250k.sty which I believe was once
> >> discussed
> >> > on the list on June 4, 2007 (see below):
> >> >
> >> >> library(oligo)
> >> >> library(pd.mapping250k.sty)
> >> >> rawData<-read.celfiles(list.celfiles())
> >> >> rma<-snprma(rawData)
> >> >
> >> >> Normalizing...Error in readChar(con, 5) : cannot open the
> >> connection
> >> >> In addition: Warning message:
> >> >> cannot open compressed file
> >> >
> >> > I am wondering if this problem was solved and if yes what was a
> >> > solution.
> >> >
> >> > Thank you in advance for your help!
> >> >
> >> > Alex
> >> >
> >> >
> >> >
> >> >
> >> >> Hi An,
> >> >>
> >> >> that's problably R complaining a file that it didn't find. The
> >> >> strange thing is that I can't reproduce it here. Could you please
> >> >> forward me the results of traceback()?
> >> >>
> >> >> This would happen if, for example, oligo finds the old version
> >> of the
> >> >> pd.mapping250k.sty package.
> >> >>
> >> >> b
> >> >
> >> > On Jun 4, 2007, at 8:07 AM, De Bondt, An-7114 [PRDBE] wrote:
> >> >
> >> >>> Hi Ben,
> >> >>>
> >> >>> When using oligo version 1.0.2-3, the pmStrand function indeed
> >> >>> works :-)
> >> >>> but the snprma function results in an error:
> >> >>>
> >> >>>      fsetSty <- read.celfiles(dir()[grep("S.CEL", dir())])
> >> >>>      rmaSty <- snprma(fsetSty)
> >> >>>
> >> >>> Normalizing...Error in readChar(con, 5) : cannot open the
> >> connection
> >> >>> In addition: Warning message:
> >> >>> cannot open compressed file
> >> >>>
> >> >>> How can I check which connection needs to be established?
> >> >>>
> >> >>> Thanks in advance for your help!
> >> >>> An
> >> >>>
> >> >
> >> > _______________________________________________
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> >>
>