[BioC] Envir. drosgenome1, GENENAME not defined?

Emmanuel Levy emmanuel.levy at gmail.com
Thu Mar 23 17:19:42 CET 2006


Dear Bioconductor community,

I just started working with the drosgenome1 environment.
When I try to get the gene names from drosgenome1GENENAME,
I only get 5 gene names and 14005 NA values.

> table(GN)
GN
         Fas (TNF receptor superfamily member)
                                             1
FBJ murine osteosarcoma viral oncogene homolog
                                             1
                                interleukin 10
                                             1
                                 interleukin 2
                                             1
                                 interleukin 4
                                             1
                                            NA
                                         14005

A couple of other environments seem to be empty (SUMFUNC, PATH ...)

Is that normal?

Many thanks in advance for your comments,

  Emmanuel

> sessionInfo()
R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
   drosgenome1 drosgenome1cdf       annotate        annaffy           KEGG
      "1.10.0"       "1.10.0"        "1.8.0"        "1.2.0"        "1.8.1"
            GO           affy        Biobase
       "1.8.2"        "1.8.1"        "1.8.0"


=====================================
drosgenome1 INSTALL INFO

> biocLite("drosgenome1")

Running bioCLite version 0.1  with R version  2.2.1

Running biocinstall version 1.1  with R version  2.2.1
trying URL 'http://www.bioconductor.org/packages/data/annotation/1.7/src/contrib/drosgenome1_1.10.0.tar.gz'
Content type 'application/x-gzip' length 3374185 bytes
opened URL
==================================================
downloaded 3295Kb

* Installing *source* package 'drosgenome1' ...
** R
** data
**  moving datasets to lazyload DB
** help
 >>> Building/Updating help pages for package 'drosgenome1'
     Formats: text html latex example
  drosgenome1                       text    html    latex
  drosgenome1ACCNUM                 text    html    latex   example
  drosgenome1CHR                    text    html    latex   example
  drosgenome1CHRLOC                 text    html    latex   example
  drosgenome1ENZYME                 text    html    latex   example
  drosgenome1GENENAME               text    html    latex   example
  drosgenome1GO                     text    html    latex   example
  drosgenome1GO2ALLPROBES           text    html    latex   example
  drosgenome1GO2PROBE               text    html    latex   example
  drosgenome1LOCUSID                text    html    latex   example
  drosgenome1MAP                    text    html    latex   example
  drosgenome1ORGANISM               text    html    latex   example
  drosgenome1PATH                   text    html    latex   example
  drosgenome1PMID                   text    html    latex   example
  drosgenome1PMID2PROBE             text    html    latex   example
  drosgenome1QC                     text    html    latex
  drosgenome1REFSEQ                 text    html    latex   example
  drosgenome1SUMFUNC                text    html    latex   example
  drosgenome1SYMBOL                 text    html    latex   example
  drosgenome1UNIGENE                text    html    latex   example
** building package indices ...
* DONE (drosgenome1)

The downloaded packages are in
        /tmp/RtmpU18540/downloaded_packages



More information about the Bioconductor mailing list