[BioC] GOStats: summary hyperGTest, count and size

[Christine Gläßer]

Dear Marc,

thank you very much for your kind and fast reply. I checked the universe 
and gene counts - same results (13, 62 genes instead of 1,1). However, 
the documentation in universeCounts clarified why I had 62 in "size" 
("‘Size’ is the number that could have been found in your gene list if 
every instance had turned up.") instead of 1; the docu further says that 
geneCounts should return the numbers of genes annotated to a specific 
term, if I understand correctly - then I would expect only 1 gene to be 
enlisted. Is there a misunderstanding on my side, and geneCounts enlists 
all genes belonging to the instances mentioned in "size", which are of 
course more genes than the one which is annotated with the specific term?

Kind regards and many thanks,

Christine Gläßer