[BioC] SNPRMA: Normalizing...Error in readChar(con, 5) : cannot open the connection
alex.lisovich at gmail.com
Mon Jun 25 17:46:00 CEST 2007
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():
R version 2.5.0 Patched (2007-05-02 r41420)
attached base packages:
 "splines" "tools" "stats" "graphics" "grDevices" "utils"
 "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"
3: readChar(con, 5)
2: load(system.file("extdata", paste(annot, "Ref.rda", sep = ""),
package = annot))
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
> 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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