Martin, Thank you--here is what I have. > annotation(sample.ExpressionSet) [1] "hgu95av2" > annotation(myAB_rma) [1] "mogene10stv1" I had library(mogene10sttranscriptcluster.db) attached so I thought that should do it? Mary Martin Morgan wrote: > On 01/27/2011 08:18 AM, Mary Putt wrote: > >> Hi >> >> I am trying to create gene sets and have the following mysterious error. >> Many thanks in advance for suggestions, >> > > Hi Mary -- > > >> Mary Putt >> >> >>> search() >>> >> [1] ".GlobalEnv" [2] >> "package:GO.db" [3] >> "package:mogene10sttranscriptcluster.db" >> [4] "package:org.Mm.eg.db" [5] >> "package:RSQLite" [6] >> "package:DBI" [7] >> "package:affy" [8] >> "package:genefilter" [9] >> "package:GSEABase" [10] >> "package:graph" [11] >> "package:annotate" [12] >> "package:AnnotationDbi" [13] >> "package:Biobase" [14] >> "package:stats" [15] >> "package:graphics" [16] >> "package:grDevices" [17] >> "package:utils" [18] >> "package:datasets" [19] >> "package:methods" [20] >> "Autoloads" [21] >> "package:base" > >> >>> date() >>> >> [1] "Thu Jan 27 11:23:25 2011" >> >>> setwd("/project/cvi/parmacek/nina_bowens/Rdata") >>> >>> load("myAB_rma.Rdata") >>> class(myAB_rma) >>> >> [1] "ExpressionSet" >> attr(,"package") >> [1] "Biobase" >> >>> objects() >>> >> [1] "e_set" "myAB_rma" >> >>> gsc<-GeneSetCollection(myAB_rma, setType=GOCollection()) >>> >> Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) : >> error in evaluating the argument 'x' in selecting a method for function >> 'as.list' >> >>> traceback() >>> >> 3: as.list(getAnnMap("GO2PROBE", annotation(idType))) >> 2: GeneSetCollection(myAB_rma, setType = GOCollection()) >> 1: GeneSetCollection(myAB_rma, setType = GOCollection()) >> > > I think the problem is that myAB_rma does not contain enough information > to create the gene set, for instance as when the 'annotation' slot of > sample.ExpressionSet is assigned a non-existent chip: > > >> data(sample.ExpressionSet) >> annotation(sample.ExpressionSet) >> > [1] "hgu95av2" > >> gsc <- GeneSetCollection(sample.ExpressionSet, setType=GOCollection()) >> annotation(sample.ExpressionSet)="foo" >> GeneSetCollection(sample.ExpressionSet, setType=GOCollection()) >> > Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) : > error in evaluating the argument 'x' in selecting a method for > function 'as.list' > > Martin > > >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >

Martin Thanks very much for the suggestion--I needed more detail on the annotation package--not just mogene10st. > annotation(myAB_rma)<-"mogene10sttranscriptcluster" > gsc<-GeneSetCollection(myAB_rma, setType=GOCollection()) Mary Martin Morgan wrote: > On 01/27/2011 08:18 AM, Mary Putt wrote: > >> Hi >> >> I am trying to create gene sets and have the following mysterious error. >> Many thanks in advance for suggestions, >> > > Hi Mary -- > > >> Mary Putt >> >> >>> search() >>> >> [1] ".GlobalEnv" [2] >> "package:GO.db" [3] >> "package:mogene10sttranscriptcluster.db" >> [4] "package:org.Mm.eg.db" [5] >> "package:RSQLite" [6] >> "package:DBI" [7] >> "package:affy" [8] >> "package:genefilter" [9] >> "package:GSEABase" [10] >> "package:graph" [11] >> "package:annotate" [12] >> "package:AnnotationDbi" [13] >> "package:Biobase" [14] >> "package:stats" [15] >> "package:graphics" [16] >> "package:grDevices" [17] >> "package:utils" [18] >> "package:datasets" [19] >> "package:methods" [20] >> "Autoloads" [21] >> "package:base" > >> >>> date() >>> >> [1] "Thu Jan 27 11:23:25 2011" >> >>> setwd("/project/cvi/parmacek/nina_bowens/Rdata") >>> >>> load("myAB_rma.Rdata") >>> class(myAB_rma) >>> >> [1] "ExpressionSet" >> attr(,"package") >> [1] "Biobase" >> >>> objects() >>> >> [1] "e_set" "myAB_rma" >> >>> gsc<-GeneSetCollection(myAB_rma, setType=GOCollection()) >>> >> Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) : >> error in evaluating the argument 'x' in selecting a method for function >> 'as.list' >> >>> traceback() >>> >> 3: as.list(getAnnMap("GO2PROBE", annotation(idType))) >> 2: GeneSetCollection(myAB_rma, setType = GOCollection()) >> 1: GeneSetCollection(myAB_rma, setType = GOCollection()) >> > > I think the problem is that myAB_rma does not contain enough information > to create the gene set, for instance as when the 'annotation' slot of > sample.ExpressionSet is assigned a non-existent chip: > > >> data(sample.ExpressionSet) >> annotation(sample.ExpressionSet) >> > [1] "hgu95av2" > >> gsc <- GeneSetCollection(sample.ExpressionSet, setType=GOCollection()) >> annotation(sample.ExpressionSet)="foo" >> GeneSetCollection(sample.ExpressionSet, setType=GOCollection()) >> > Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) : > error in evaluating the argument 'x' in selecting a method for > function 'as.list' > > Martin > > >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >