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

[James W. MacDonald]

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-
> 
> 
> 
> 
> 

-- 
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