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

[Benilton Carvalho]

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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>>