Hi, I'm using the affy HG-U133A_2_annot_csv.zip annotation file to annotate my data (which may be a bad idea to begin with..?), and would like to be able to use the GO slim categories to annotate my data (see http://www.spatial.maine.edu/~mdolan/MGI_GO_Slim.html), instead of the extremely detailed GO categories already present in the affymetrix file - Gene.Ontology.Biological.Process, Gene.Ontology.Cellular.Component, Gene.Ontology.Molecular.Function. Basically, the issue is that I don't want to have the 2,000 - 5,000 different annotation groups in my file. I want to be able to run subset() on very general groups, like "development" or "death". Thanks in advance, Ken

Ken, You could certainly produce such a list by repeating what they have done on that website. For example, for GO_slim, biologic process 3 (cell cycle and proliferation): library(hgu133a) library(annotate) genes <- unlist(lookUp(c('GO:0007049','GO:0008283'),'hgu133a','GO2ALLPROBES')) genes <- genes[!duplicated(genes)] This will contain the genes in cell cycle and proliferation. It wouldn't be hard to automate this process for each category. For those categories that include EXCLUDE descriptions, you can use R set commands like %in% to get the sets you want. Sean On Feb 24, 2005, at 11:44 AM, Ken Termiso wrote: > Hi, > > I'm using the affy HG-U133A_2_annot_csv.zip annotation file to > annotate my data (which may be a bad idea to begin with..?), and would > like to be able to use the GO slim categories to annotate my data (see > http://www.spatial.maine.edu/~mdolan/MGI_GO_Slim.html), instead of the > extremely detailed GO categories already present in the affymetrix > file - Gene.Ontology.Biological.Process, > Gene.Ontology.Cellular.Component, Gene.Ontology.Molecular.Function. > > Basically, the issue is that I don't want to have the 2,000 - 5,000 > different annotation groups in my file. I want to be able to run > subset() on very general groups, like "development" or "death". > > Thanks in advance, > Ken > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor