Greetings, I am using the GOstats package to identify significant association with GO terms of a set of "interesting" sequences NOT identified by a microarray. As far as I can tell, I have set up the vectors for the gene universe and "interesting" genes correctly. However, I am not sure what to specify for the 'annotation' parameter of the GOHyperGParams object. The vignettes use the "hgu95av2" Affymetrix chip annotation package as an example. Would be this be appropriate to use if my interesting genes were not taken from a microarray study? If not, is it possible to use some other environment (in the GO library perhaps)? I have already tried specifying "GOENTREZID2" as the annotation package, but I receive the following error message and think I am missing something: ""Error in get(x, envir, mode, inherits) : variable "GOENTREZID2ENTREZID" of mode "environment" was not found"" Do I need to specify a new variable for the Entrez IDs? Any advice would be greatly appreciated on how to set the annotation parameter for the hyperGTest. Thank you. Michael

Hi Michael, Michael Mayhew wrote: > Greetings, > > I am using the GOstats package to identify significant association with GO > terms of a set of "interesting" sequences NOT identified by a microarray. > > As far as I can tell, I have set up the vectors for the gene universe and > "interesting" genes correctly. However, I am not sure what to specify for the > 'annotation' parameter of the GOHyperGParams object. You will need an annotation package from which you will extract the GO information for the test (Seth Falcon may have a way around this, but AFAIK there is none). You will need to build one using the AnnBuilder package, based on whatever you used to come up with the list of genes that you are using. It might be simpler to use the Category package to do this (but regardless, you need to have mappings of genes to GO terms from some source. Best, Jim -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.