[BioC] Problems when access elements in mogene10stprobeset.db

Peng Yu pengyu.ut at gmail.com
Thu Aug 6 21:18:56 CEST 2009


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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