Question: Human Gene 1.0 ST array
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gravatar for Chandra Sekhar
10.8 years ago by
Chandra Sekhar10 wrote:
Hi, I would like to extract gene names (featureNames) using annaffy, but i am unable to find Affymetrix probe sequence and annotation data for Human Gene 1.0 ST array. Installed bioconductor version 2.2 and R version 2.7.2. I tried below link (2.3 devel), apparently it gives Error: AnnotationDbi version is 1.2.2 , >= 1.3.x is needed by hugene10st http://www.bioconductor.org/packages/2.3/data/annotation/html/hugene10 st.db.html (CEL files belonging to human gene 1.0 st array) rawdata<-ReadAffy() symbols<-aafSymbol(featureNames(rawdata),"hugene10st.db") I could successfully perform the same operation using Affymetrix Human Genome U133 Plus 2.0 Array (CEL files belonging to U133) symbols<-aafSymbol(featureNames(rawdata),"hgu133plus2") Please let me know if Human gene 1.0 ST array is supported. Thanks, Chandra
annotation probe annaffy • 2.6k views
ADD COMMENTlink modified 10.8 years ago by James W. MacDonald50k • written 10.8 years ago by Chandra Sekhar10
Answer: Human Gene 1.0 ST array
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gravatar for James W. MacDonald
10.8 years ago by
United States
James W. MacDonald50k wrote:
Hi Chandra, Chandra Sekhar wrote: > Hi, > > I would like to extract gene names (featureNames) using annaffy, but > i am unable to > find Affymetrix probe sequence and annotation data for Human Gene 1.0 > ST array. Installed > bioconductor version 2.2 and R version 2.7.2. > > I tried below link (2.3 devel), apparently it gives Error: > AnnotationDbi version is 1.2.2 , >= 1.3.x > is needed by hugene10st Yes. If you want to use the devel version of BioC, you need to use the devel version of R. Since both will be released within weeks, there is really no reason not to upgrade. Best, Jim > > http://www.bioconductor.org/packages/2.3/data/annotation/html/hugene 10st.db.html > > (CEL files belonging to human gene 1.0 st array) > rawdata<-ReadAffy() > symbols<-aafSymbol(featureNames(rawdata),"hugene10st.db") > > I could successfully perform the same operation using Affymetrix Human > Genome U133 Plus 2.0 Array > (CEL files belonging to U133) > > symbols<-aafSymbol(featureNames(rawdata),"hgu133plus2") > > Please let me know if Human gene 1.0 ST array is supported. > > Thanks, > Chandra > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD COMMENTlink written 10.8 years ago by James W. MacDonald50k
Just going by the error message, you will also need the development version of AnnotationDbi. Although I think Jim's point was that it would be good to just upgrade everything, which is great advice since that is how these things are tested (ie. within a release). Marc James W. MacDonald wrote: > Hi Chandra, > > Chandra Sekhar wrote: >> Hi, >> >> I would like to extract gene names (featureNames) using annaffy, but >> i am unable to >> find Affymetrix probe sequence and annotation data for Human Gene 1.0 >> ST array. Installed >> bioconductor version 2.2 and R version 2.7.2. >> >> I tried below link (2.3 devel), apparently it gives Error: >> AnnotationDbi version is 1.2.2 , >= 1.3.x >> is needed by hugene10st > > Yes. If you want to use the devel version of BioC, you need to use the > devel version of R. Since both will be released within weeks, there is > really no reason not to upgrade. > > Best, > > Jim > > >> >> http://www.bioconductor.org/packages/2.3/data/annotation/html/hugen e10st.db.html >> >> >> (CEL files belonging to human gene 1.0 st array) >> rawdata<-ReadAffy() >> symbols<-aafSymbol(featureNames(rawdata),"hugene10st.db") >> >> I could successfully perform the same operation using Affymetrix Human >> Genome U133 Plus 2.0 Array >> (CEL files belonging to U133) >> >> symbols<-aafSymbol(featureNames(rawdata),"hgu133plus2") >> >> Please let me know if Human gene 1.0 ST array is supported. >> >> Thanks, >> Chandra >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.8 years ago by Marc Carlson7.2k
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