[BioC] YGS98 package does not provide locus link ID information ?

[Marc Carlson]

James W. MacDonald wrote:
> Hi Alex,
>
> It would help if you gave us your sessionInfo(). I checked both BioC 2.0 
> and BioC 2.1 versions of this package and neither had either a 
> ygs98LOCUSID nor a ygs98ENTREZID, which makes me think you have a really 
> old version of R and BioC.
>
> I don't do much yeast stuff, but I was under the impression that Entrez 
> Gene didn't really pertain to this species. But maybe some of the yeast 
> people out there can comment on that.
>
> Best,
>
> Jim
>
>
>
> Alex Tsoi wrote:
>   
>> Dear all,
>>
>> I am trying to use the ygs98 package to annotate the probesets from the
>> YGS98 microarray platform, however, I figure out that the annotation package
>> does not provide any information about the Locus Link ID / ENTREZ ID:
>>
>>     
>>> ls("package:ygs98")
>>>       
>>  [1] "ygs98"             "ygs98ALIAS"        "ygs98CHR"
>>  [4] "ygs98CHRLENGTHS"   "ygs98CHRLOC"       "ygs98DESCRIPTION"
>>  [7] "ygs98ENZYME"       "ygs98ENZYME2PROBE" "ygs98GENENAME"
>> [10] "ygs98GO"           "ygs98GO2ALLPROBES" "ygs98GO2PROBE"
>> [13] "ygs98LOCUSID"      "ygs98MAPCOUNTS"    "ygs98ORF"
>> [16] "ygs98ORGANISM"     "ygs98PATH"         "ygs98PATH2PROBE"
>> [19] "ygs98PMID"         "ygs98PMID2PROBE"   "ygs98QC"
>> [22] "ygs98QCDATA"
>>
>> The package does contain ygs98LOCUSID, but when I try to get information
>> from it:
>>
>>     
>>> unlist(as.list(ygs98LOCUSID))
>>>       
>> Error in function ()  : object "ygs98ENTREZID" not found
>> In addition: Warning message:
>> 'ygs98LOCUSID' is deprecated.
>> Use 'ygs98ENTREZID' instead.
>> See help("Deprecated")
>>
>> However, ygs98ENTREZID in fact does not exist.......
>>
>>
>>
>> Could anyone show me some ways I could find the locus link / entrezid ID
>> directly if I have a set of probesets from the ygs98 microarray platform ?
>>
>> Thanks a lot,
>> Alex-
>>     

I have tested this out, and I don't see any evidence of locuslink IDs in
the most recent versions of these packages. They are not even mentioned
anymore, so Jim is probably correct about your packages being old, as
these fields were deprecated a long time ago. The reason that they were
taken out was lack of demand. It seems that there are very few people in
the yeast community who regularly use Entrez Gene IDs which rendered
them into a sort of dead-end for most annotation purposes.

If Entrez gene IDs are truly valuable for this species, then I am more
than willing to entertain putting them back into the development version
of these packages. Can please provide me with a purpose for these IDs by
telling me what you were planning to do with them?

Marc