[BioC] Envir. drosgenome1, GENENAME not defined?

[Ting-Yuan Liu]

Hi Emmanuel,

I just notice that even thought there are only 5 gene names in this 
package, there are still 13252 SYMBOLs: 

drosgenome1SYMBOL found 13252 of 14010

I believe they are as useful as GENENAMEs:

> head(as.list(drosgenome1SYMBOL))
$`155157_at`
[1] "CycG"

$`155122_at`
[1] "CG9411"

$`155036_at`
[1] "CG1416"

$`154985_at`
[1] "CG9083"

$`154948_at`
[1] "eIF2B-epsilon"

$`154899_at`
[1] "lid"

It seems that NCBI only provide the gene symbols for these probes in the 
downloadable files.  I don't think we can do anything on this unless NCBI 
provides them.  

HTH,
Ting
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Thu, 23 Mar 2006, 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?
> 
> 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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