[BioC] probesets from a KEGGHyperGParams instance

[Louisa A Rispoli/AS/EXP/UTIA]

Jim-

Thank you for the prompt reply. I am using affy ids and performing the
analysis similar to your description. I was just trying to figure out if
there was a way to append the htmlReport to include the geneIDsByCategory
or affy probes without making my head or computer explode. Thank you again
for the help.

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




                                                                           
             "James W.                                                     
             MacDonald"                                                    
             <jmacdon at med.umic                                          To 
             h.edu>                    Louisa A Rispoli/AS/EXP/UTIA        
                                       <larispoli at mail.ag.utk.edu>         
             10/30/2008 03:24                                           cc 
             PM                        bioconductor at stat.math.ethz.ch      
                                                                   Subject 
                                       Re: [BioC] probesets from a         
                                       KEGGHyperGParams instance           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




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
results.

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
[snip..]

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"
"1269_at"
  [7] "1322_at"   "1504_s_at" "1542_at"   "1526_i_at" "1570_f_at"
"1713_s_at"


Best,

Jim

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.
Biostatistician
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