[BioC] Envir. drosgenome1, GENENAME not defined?

[James W. MacDonald]

Emmanuel Levy wrote:
> 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?

I don't know about normal, but it is correct:

 > drosgenome1()


Quality control information for  drosgenome1
Date built: Created: Wed Jan  4 18:17:19 2006

Number of probes: 14010
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
          drosgenome1ACCNUM found 14010 of 14010
          drosgenome1CHRLOC found 13244 of 14010
          drosgenome1CHR found 13252 of 14010
          drosgenome1ENZYME found 0 of 14010
          drosgenome1GENENAME found 5 of 14010  <===== only 5 names
          drosgenome1GO found 8749 of 14010
          drosgenome1LOCUSID found 13252 of 14010
          drosgenome1MAP found 13233 of 14010
          drosgenome1PATH found 0 of 14010
          drosgenome1PMID found 13252 of 14010
          drosgenome1REFSEQ found 13249 of 14010
          drosgenome1SUMFUNC found 0 of 14010
          drosgenome1SYMBOL found 13252 of 14010
          drosgenome1UNIGENE found 13129 of 14010
Mappings found for non-probe based rda files:
          drosgenome1GO2ALLPROBES found 5586
          drosgenome1GO2PROBE found 4063
          drosgenome1ORGANISM found 1
          drosgenome1PMID2PROBE found 9353

I don't know why there aren't more names, considering most of the really 
cool gene names come from the fly guys (frizzled, sonic hedgehog, son of 
sevenless, etc). Maybe Ting knows why there are so few names?

Best,

Jim


> 
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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