[BioC] which universe in hyperGTest

[James W. MacDonald]

marco zucchelli wrote:
> 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)

You want the unique genes. In addition, if you have done any 
pre-filtering of the data to remove e.g., those genes that don't change 
expression, you want to remove those from your universe as well. The 
universe should only consist of unique genes that could have been 
selected by whatever statistical test you used. BTW, the geneIds should 
also be unique.

Seth has made some changes to the GOstats vignette that should make all 
of this quite clear:

http://www.bioconductor.org/packages/2.0/bioc/vignettes/GOstats/inst/doc/GOstatsHyperG.pdf

Best,

Jim


> 
> in the GOHyperGParams ??
> 
> Regards
> 
> Marco
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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