[BioC] Problems when access elements in mogene10stprobeset.db

[Peng Yu]

Hi,

I run the following command, which still give me the same error.

Rscript --no-init-file mogeneID.R

Can somebody let me know how to figure out what the problems are? Is
there any hiden BioC information that may be shown to pinpoint the
problems?

Regards,
Peng

On Thu, Aug 6, 2009 at 4:41 PM, Marc Carlson<mcarlson at fhcrc.org> wrote:
> Hi Peng,
>
> I have run the following;
>
> library(mogene10stprobeset.db)
> sessionInfo()
> all_probes<-ls(mogene10stprobesetENTREZID)
> set.seed(0xa1beef)
> probes <-sample(all_probes, 5)
> print(probes)
> mogene10stprobesetENTREZID[[probes[1]]]
>
>
> And it runs fine for me.  So I don't think there is anything wrong with
> your R script, unless there is more than you have shown us here.  The
> one thing I noticed was that my version of R was slightly newer than
> yours.  But a problem like you report here should have alerted a lot
> more people if it were caused by R.
>
>  Marc
>
>
>
> Peng Yu wrote:
>> Hi,
>>
>> Below this email is the R script and the output that I got after
>> running the script. Can somebody take a look help me figure out why I
>> get an error message? I followed in the instructions in
>> AnnotationDbi.pdf.
>>
>> Regards,
>> Peng
>>
>> $ cat mogeneID.R
>> library(mogene10stprobeset.db)
>> sessionInfo()
>> all_probes<-ls(mogene10stprobesetENTREZID)
>> set.seed(0xa1beef)
>> probes <-sample(all_probes, 5)
>> print(probes)
>> mogene10stprobesetENTREZID[[probes[1]]]
>>
>> $ Rscript mogeneID.R
>> Loading required package: methods
>> Loading required package: Biobase
>> Loading required package: utils
>>
>> Welcome to Bioconductor
>>
>>   Vignettes contain introductory material. To view, type
>>   'openVignette()'. To cite Bioconductor, see
>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: affy
>> Loading required package: affyio
>> Loading required package: AnnotationDbi
>> Loading required package: DBI
>> R version 2.9.1 (2009-06-26)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>
>> other attached packages:
>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>> [3] DBI_0.2-4                   AnnotationDbi_1.6.1
>> [5] makecdfenv_1.22.0           affyio_1.12.0
>> [7] affy_1.22.1                 Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] preprocessCore_1.6.0
>> [1] "10377734" "10527109" "10489285" "10353981" "10371859"
>> Error in names(colnames) <- colmetanames(x) :
>>   attempt to set an attribute on NULL
>> Calls: [[ ... as.list -> as.list -> .tagCol -> tagname -> tagname
>> Execution halted
>>
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>>
>
>