[BioC] GoHyperG question

Carri-Lyn Mead carri-lyn at bioinformatics.ubc.ca
Tue Aug 3 21:32:58 CEST 2004


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



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