Question: GO with mu11ksuba(b)
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gravatar for Mayte Suarez-Farinas
14.5 years ago by
Mayte Suarez-Farinas300 wrote:
Hi, I was trying to use the GO package with the mouse chips mu11ksuba and mu11ksubb. The following two functions: res<-getGO(probesids[1:100],'mu11ksuba') res<-unique(lookUp('GO:0006338','mu11ksuba',"GO2ALLPROBES")) gave the same error: Error in package_version(vers) : invalid version spec But it works just fine with hgu95av2, res<-unique(lookUp('GO:0006338','hgu95av2',"GO2ALLPROBES")) I reinstalled all BioC developmental package and the cdf and probe packages for mu11ksuba(b) chips again and I still got the same error. Any hint ?? Thanks in advance, -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422
go hgu95av2 mu11ksuba cdf • 386 views
ADD COMMENTlink modified 14.5 years ago by Seth Falcon7.4k • written 14.5 years ago by Mayte Suarez-Farinas300
Answer: GO with mu11ksuba(b)
0
gravatar for John Zhang
14.5 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>I was trying to use the GO package with the mouse chips mu11ksuba and >mu11ksubb. The following two functions: > > res<-getGO(probesids[1:100],'mu11ksuba') > res<-unique(lookUp('GO:0006338','mu11ksuba',"GO2ALLPROBES")) > >gave the same error: > > Error in package_version(vers) : invalid version spec > >But it works just fine with hgu95av2, > > res<-unique(lookUp('GO:0006338','hgu95av2',"GO2ALLPROBES")) > >I reinstalled all BioC developmental package and the cdf and probe >packages for mu11ksuba(b) chips again and I still got the same error. You need to have the mu11ksuba annotation data package installed. Currently Bioconductor does not have a data package for mu11ksuba but you can always build one yourself using the AnnBuilder package. > > >Any hint ?? > >Thanks in advance, > >-- >Mayte Suarez Farinas >The Rockefeller University >1230 York Avenue, Box 212 >New York, NY 10021 >phone: 1-212-327-8186 >fax: 1-212-327-7422 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 14.5 years ago by John Zhang2.9k
Answer: GO with mu11ksuba(b)
0
gravatar for Seth Falcon
14.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Mayte Suarez-Farinas <mayte@babel.rockefeller.edu> writes: > Hi, > I was trying to use the GO package with the mouse chips mu11ksuba and > mu11ksubb. The following two functions: > > res<-getGO(probesids[1:100],'mu11ksuba') > res<-unique(lookUp('GO:0006338','mu11ksuba',"GO2ALLPROBES")) > > gave the same error: > > Error in package_version(vers) : invalid version spec > > But it works just fine with hgu95av2, > > res<-unique(lookUp('GO:0006338','hgu95av2',"GO2ALLPROBES")) > > I reinstalled all BioC developmental package and the cdf and probe > packages for mu11ksuba(b) chips again and I still got the same error. > > > Any hint ?? I think we don't have an annotation data package for the mu11ksuba chip and that is what the error message is (trying) to tell you. + seth
ADD COMMENTlink written 14.5 years ago by Seth Falcon7.4k
Hi, The biomaRt package (see developmental packages) provides annotation for mu11ksuba. In biomaRt your query would be: mart<-martConnect() res<-getGO(id=probeids[1:100], array="mu11ksuba",mart=mart) best, Steffen Seth Falcon wrote: >Mayte Suarez-Farinas <mayte@babel.rockefeller.edu> writes: > > > >>Hi, >>I was trying to use the GO package with the mouse chips mu11ksuba and >>mu11ksubb. The following two functions: >> >> res<-getGO(probesids[1:100],'mu11ksuba') >> res<-unique(lookUp('GO:0006338','mu11ksuba',"GO2ALLPROBES")) >> >>gave the same error: >> >> Error in package_version(vers) : invalid version spec >> >>But it works just fine with hgu95av2, >> >> res<-unique(lookUp('GO:0006338','hgu95av2',"GO2ALLPROBES")) >> >>I reinstalled all BioC developmental package and the cdf and probe >>packages for mu11ksuba(b) chips again and I still got the same error. >> >> >>Any hint ?? >> >> > >I think we don't have an annotation data package for the mu11ksuba >chip and that is what the error message is (trying) to tell you. > >+ seth > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
ADD REPLYlink written 14.5 years ago by Steffen Durinck420
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