[BioC] GOstats testing using EntrezGene IDs not in chip-specific annotation package?

[Jenny Drnevich]

Hi everyone,

A colleague of mine has been using BioC to do his analyses on his 
custom stickleback array, and asked me to check to make sure he was 
doing everything correctly. I'm not sure about one part, so I'm 
asking the list.  The stickleback genome is not well annotated in 
regards to GO terms, but he has mapped all the stickleback microarray 
probes to zebrafish EntrezGene IDs. Instead of making his own 
chip-specific AnnotationDBI package, he's doing GO testing using the 
zebrafish.db packages from BioC. Everything seems to be running fine 
and there are no error messages, but I'm not sure if there aren't 
some hidden problems.

For example, what if some of his zebrafish EntrezGene IDs are not on 
the Affy zebrafish array? Would it be fine as long as they were in 
the org.Dr.eg.db based data package?  According to the GOstats 
vignette on Hypergeometric Tests, when you set up your GOHyperGParams 
object, you have to specify a chip-specific AnnotationDBI package, 
but you input your selected genes and universe as (usually) 
EntrezGene IDs, not probe set IDs. This makes me wonder if hyperGTest 
is doing everything through the zebrafish.db package, or going 
directly to the org.Dr.eg.db package?

He hasn't checked yet to see if all of his EntrezGene IDs are or are 
not on the Affy zebrafish array, and if they are then I guess there 
is no problem in simply using the zebrafish.db package. Mainly my 
question is why does the GOstats hyperGTest() require a chip-specific 
annotation package when you have to input EntrezGene IDs (the 
mapping  key for the org.Xx.eg.db packages), not probe set 
IDs?  Could hyperGTest()  be (easily) modified to directly accept the 
org.Xx.eg.db packages?

Thanks,
Jenny

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu