Hello, Please excuse this naive question, but I would appreciate if someone could point me at the right function(s) to use: I have two vectors containing all GO terms associated with proteins retrieved in two proteomic experiments and would like to figure out for which categories they differ significantly from each other. I am obviously somewhat limited by the fact of not being able to use the 'standard' annotation packages, but I have build my own protein -> GenBank -> GO package using AnnBuilder. Please let me know how you would tackle this. Thanks for your patience, Joh

Johannes Graumann wrote: > Hello, > > Please excuse this naive question, but I would appreciate if someone could > point me at the right function(s) to use: > I have two vectors containing all GO terms associated with proteins > retrieved in two proteomic experiments and would like to figure out for > which categories they differ significantly from each other. I am obviously > somewhat limited by the fact of not being able to use the 'standard' > annotation packages, but I have build my own protein -> GenBank -> GO > package using AnnBuilder. > > Please let me know how you would tackle this. > > Thanks for your patience, > > Joh Dear Johannes, not sure whether the existing software provides directly for your question, or whether indeed I fully understand your question, but if I do, one option would be simply to do a Binomial test against the Null hypothesis a[i] ~ Bin( a[i]+b[i], p=0.5) where a[i] : frequency of GO Term i in Experiment A b[i] : frequency of GO Term i in Experiment B This can be done just using the function "pbinom". Or to consider the z-scores (a-b) / sqrt(a+b) Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber