[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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