[BioC] probesets from a KEGGHyperGParams instance

James W. MacDonald jmacdon at med.umich.edu
Thu Oct 30 20:23:56 CET 2008

Hi Louisa,

With the new SQLite-based annotation packages this should be much more 
simple, although there isn't anything that I know of to give you direct 

Since you use the term 'probeset' I will take the liberty of assuming 
you are using an Affy chip of some sort. Let's say you have a vector of 
significant probesets that you used to do the hypergeometric analysis. 
You then converted to Entrez Gene IDs and then did the KEGG 
hypergeometric analysis. An example:

## fake up some data
 > library(GOstats)
 > library(hgu95av2.db)
 > probeids <- Lkeys(hgu95av2PATH[sample(1:1000, 200)])
 > egids <- unique(getEG(probeids, "hgu95av2"))
 > univ <- unique(getEG(Lkeys(hgu95av2PATH), "hgu95av2"))
 > p <- new("KEGGHyperGParams", geneIds = egids, universeGeneIds = univ, 
annotation = "hgu95av2")
 > hypt <- hyperGTest(p)
 > summary(hypt)
    KEGGID       Pvalue OddsRatio  ExpCount Count Size Term
1   05218 1.992936e-07  8.600189 1.8950675    12   58 Melanoma

You can also get a nice HTML output using htmlReport():

 > htmlReport(hypt, file="output.html",summary.args=list(htmlLinks=TRUE))

So let's say we are completely enthralled with that first term (because 
we are skin cancer researchers and stuff ;-D). Let's see what probeids 
in our significant set map to that term:

 > prbs <- probeids[probeids %in% get("05218", revmap(hgu95av2PATH))]
 > prbs
  [1] "1706_at"   "1654_at"   "1593_at"   "1859_s_at" "1340_s_at" 
  [7] "1322_at"   "1504_s_at" "1542_at"   "1526_i_at" "1570_f_at" 



Louisa A Rispoli/AS/EXP/UTIA wrote:
> To anyone with a lot more experience.
> I have been trying to read through all the helps and vignettes for a simple
> way to get the probesets that went into producing significance of KEGG term
> after running hypergeometric test for KEGG. I have found probeSetSummary
> for GO terms and hyperGoutput (also for GO terms) but nothing corresponding
> for the KEGG. Was hoping someone had a simple methodology for retrieval.
> Thanks
> Louisa
> "If we knew what we were doing, it wouldn't be called Research." - Albert
> Einstein
> Louisa Rispoli, Ph.D. Reproductive Physiology
> Department of Animal Science
> University of Tennessee, Knoxville
> A105 Johnson Animal Research and Teaching Unit
> 1750 Alcoa Highway
> Knoxville, TN 37920
> phone:(865) 946-1874
> fax:(865) 946-1010
> email: lrispoli at utk.edu
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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