Question: Yeast and LocuslinkIDs
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gravatar for Christina Kendziorski
14.7 years ago by
Christina Kendziorski60 wrote:
Hi all, We are trying to use GOHyperG on yeast. The problem seems to be that there is no yeast2locuslinkid function, and GOHyperG expects locuslink ids. I cannot seem to find an easy way to go from yeast probe set ids to locuslink ids. Is there a way ? We are currently trying to work something out using GOALLLOCUSID. Thanks, Christina Christina Kendziorski Assistant Professor Department of Biostatistics and Medical Informatics University of Wisconsin - Madison Medical Sciences Center (6729) 1300 University Avenue Madison, Wisconsin 53706 Phone: (608) 262-3146 Fax: (608) 265-7916
go yeast • 377 views
ADD COMMENTlink modified 14.7 years ago by Sean Davis21k • written 14.7 years ago by Christina Kendziorski60
Answer: Yeast and LocuslinkIDs
0
gravatar for Sean Davis
14.7 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
What chip are you using? Sean On Jan 21, 2005, at 4:08 PM, Christina Kendziorski wrote: > > > > Hi all, > > We are trying to use GOHyperG on yeast. The problem seems to be that > there is no yeast2locuslinkid function, and GOHyperG expects > locuslink ids. I cannot seem to find an easy way to go from yeast > probe set ids to locuslink ids. > > Is there a way ? We are currently trying to work something out using > GOALLLOCUSID. > > Thanks, > > Christina > > Christina Kendziorski > Assistant Professor > Department of Biostatistics and Medical Informatics > University of Wisconsin - Madison > Medical Sciences Center (6729) > 1300 University Avenue > Madison, Wisconsin 53706 > > Phone: (608) 262-3146 > Fax: (608) 265-7916 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 14.7 years ago by Sean Davis21k
Affy yeast genome s98 Christina Christina Kendziorski Assistant Professor Department of Biostatistics and Medical Informatics University of Wisconsin - Madison Medical Sciences Center (6729) 1300 University Avenue Madison, Wisconsin 53706 Phone: (608) 262-3146 Fax: (608) 265-7916 On Fri, 21 Jan 2005, Sean Davis wrote: > What chip are you using? > > Sean > > On Jan 21, 2005, at 4:08 PM, Christina Kendziorski wrote: > > > > > > > > > Hi all, > > > > We are trying to use GOHyperG on yeast. The problem seems to be that > > there is no yeast2locuslinkid function, and GOHyperG expects > > locuslink ids. I cannot seem to find an easy way to go from yeast > > probe set ids to locuslink ids. > > > > Is there a way ? We are currently trying to work something out using > > GOALLLOCUSID. > > > > Thanks, > > > > Christina > > > > Christina Kendziorski > > Assistant Professor > > Department of Biostatistics and Medical Informatics > > University of Wisconsin - Madison > > Medical Sciences Center (6729) > > 1300 University Avenue > > Madison, Wisconsin 53706 > > > > Phone: (608) 262-3146 > > Fax: (608) 265-7916 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >
ADD REPLYlink written 14.7 years ago by Christina Kendziorski60
Christina, Did you load your data using affy? Someone with more affy experience might chime in here, but does the affy package pull anything besides the cdf package automatically? In any case, there is an annotation package available at http://www.bioconductor.org/data/metaData/yg98_1.6.8.tar.gz You can download and install it and then use the tools in the 'annotate' package to query for locusids. Hope this helps, Sean On Jan 21, 2005, at 4:31 PM, Christina Kendziorski wrote: > > > Affy yeast genome s98 > > Christina > > Christina Kendziorski > Assistant Professor > Department of Biostatistics and Medical Informatics > University of Wisconsin - Madison > Medical Sciences Center (6729) > 1300 University Avenue > Madison, Wisconsin 53706 > > Phone: (608) 262-3146 > Fax: (608) 265-7916 > > > On Fri, 21 Jan 2005, Sean Davis wrote: > >> What chip are you using? >> >> Sean >> >> On Jan 21, 2005, at 4:08 PM, Christina Kendziorski wrote: >> >>> >>> >>> >>> Hi all, >>> >>> We are trying to use GOHyperG on yeast. The problem seems to be that >>> there is no yeast2locuslinkid function, and GOHyperG expects >>> locuslink ids. I cannot seem to find an easy way to go from yeast >>> probe set ids to locuslink ids. >>> >>> Is there a way ? We are currently trying to work something out using >>> GOALLLOCUSID. >>> >>> Thanks, >>> >>> Christina >>> >>> Christina Kendziorski >>> Assistant Professor >>> Department of Biostatistics and Medical Informatics >>> University of Wisconsin - Madison >>> Medical Sciences Center (6729) >>> 1300 University Avenue >>> Madison, Wisconsin 53706 >>> >>> Phone: (608) 262-3146 >>> Fax: (608) 265-7916 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>
ADD REPLYlink written 14.7 years ago by Sean Davis21k
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