Hi List, I am currently working on a project where I have a select list of human genes and I want to see if they are statistically overrepresented in any GO category when compared to the entire human genome. To do this, I wish to use bioconductor. So far I have R version 1.9.0 installed as well as various bioconductor packages. I believe the GOHyperG function in the GOstats package would do what I want. An example of what I've tried as a test: require(GOstats) library(humanLLMappings) x <- c("392316", "60", "53467", "32") GOHyperG(x, "humanLLMappings", "MF") And I get the error: Error in get(x, envir, mode, inherits) : variable "humanLLMappingsLOCUSID" of mode "environment" was not found I have 2 questions: 1. for the test I want to do (comparison against all human genes), is HumanLLMappings the appropriate set to use, or should I be making my own with AnnBuilder? 2. What am I doing wrong above? Why do I get the environment error? Any help you can give would be much appreciated Thanks Carri-Lyn Mead

>require(GOstats) >library(humanLLMappings) >x <- c("392316", "60", "53467", "32") >GOHyperG(x, "humanLLMappings", "MF") > >And I get the error: >Error in get(x, envir, mode, inherits) : >variable "humanLLMappingsLOCUSID" of mode "environment" was not found The second argument to GOHyper is supposed to be the name for a BioC annotation data package for a given platform. "humanLLMappings" is not an annotation package for any platform. > >I have 2 questions: >1. for the test I want to do (comparison against all human genes), is >HumanLLMappings the appropriate set to use, or should I be making my >own with AnnBuilder? No, humanLLMappings is not the right package. You will have to build an annotation package for the genes you are interested in. > >2. What am I doing wrong above? Why do I get the environment error? See above. > >Any help you can give would be much appreciated >Thanks >Carri-Lyn Mead > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084