[BioC] GoHyperG question

[John Zhang]

>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
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084