[BioC] Problems when access elements in mogene10stprobeset.db

Marc Carlson mcarlson at fhcrc.org
Thu Aug 6 23:41:16 CEST 2009


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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