Hi,

 I am using hyperGTest to test GO. Fot the universe of genes I use the
follwing:

ENTREZ      <- as.list(hgu133plus2ENTREZID)
univ        <- unlist(ENTREZ)
univ        <- univ[!is.na(univ)]

now in univ there are 47,430 genes but only 19,871 are unique, since the
same gene can be hybrydized several times on the same array.

> length(univ)
[1] 47430
> length(unique(univ))
[1] 19871


Is it correct to have repetitions or should a list of unique genes be used?
i.e. should I use:

universeGeneIds=univ   or
universeGeneIds=unique(univ)

in the GOHyperGParams ??

Regards

Marco

	[[alternative HTML version deleted]]

