[BioC] a question for Metadata package: hgu133a

[Nianhua Li]

Shi, Tao <shidaxia at ...> writes:

> 
> Hi list,
> 
> Please see the following:
> 
> > package.version('hgu133a')
> [1] "1.12.0"
> > get('202990_at',  hgu133aGENENAME)
> [1] "phosphorylase, glycogen"                                 " liver (Hers 
disease, glycogen storage disease type VI)"
> > get('202100_at',  hgu133aGENENAME)
> [1] "v-ral simian leukemia viral oncogene homolog B (ras related"
> [2] " GTP binding protein)" 
> 
> > get('202990_at',  hgu133aGENENAME)[1]
> [1] "phosphorylase, glycogen"
> > get('202990_at',  hgu133aGENENAME)[2]
> [1] " liver (Hers disease, glycogen storage disease type VI)"
> 
> > get('202100_at',  hgu133aGENENAME)[1]
> [1] "v-ral simian leukemia viral oncogene homolog B (ras related"
> > get('202100_at',  hgu133aGENENAME)[2]
> [1] " GTP binding protein)"
> 
> I understand that b/c there were ";" in the original annotations, the two 
parts were put into two separate
> fields.  But does it make more sense just to combine them into one?  It will 
make coding much easier.
> 
> ...Tao
> 
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> 
> 
Hi, Tao,

Thanks for the bug report. I will try to fix it next week. In package hgu133a, 
one probe set ID only maps to one Entrez Gene ID therefore should have only one 
gene name. So, a silly, temporary work around would be:

x <- get('202100_at', hgu133aGENENAME)
x <- paste(x, sep="", collapse="")

Sorry for the inconvenience. If you also observe other problems in hgu133a, 
please let us know so that we can fix them all together. Many thanks.

nianhua

Nianhua Li
Computational Biology, PHS, FHCRC