[BioC] GOstats - hyperGTest using "KEGGHyperGParams"

[Robert Gentleman]

Hi Paul,
   Thanks for the bug report, it seems that there is an issue when all 
values are zero, which shows up intermittently.  You can solve it by 
using try or tryCatch around the call to hyperGTest.  You can simply use 
a p-value of 1, which is what it will be.

You should not be loading the GO package for this (KEGG if anything, and 
even then, please use KEGG.db, not KEGG).

   I will fix the bug, but given how close the release is I won't back 
port it, and it will only be available in the devel branch (soon to be 
the release branch),

   best wishes
    Robert

Paul Evans wrote:
> Hi all,
> 
> I was trying to understand the hyperGTest for KEGG, and used the following code:
> 
> -----------------------------------------------------------------------------------------------------------
> ## TEST HYPERGTEST FOR KEGG
> 
> library("YEAST")
> library("GOstats")
> library("GO")
> 
> # Convert to a list
> xx <- as.list(YEASTGENENAME)
> # Remove probes that do not map to any GENENAME
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
>    # Gets the gene names for the first five probe identifiers
>    xx[1:5]
>    # Get the first one
>    xx[[1]]
> }
> 
> ## Create gene universe
> allGenes <- names(xx)
> print(length(allGenes))
> geneUniverse <- allGenes[1:800]
> for(i in 1:20){
>     ## Create random cluster of 13 genes
>     geneCluster <- sample(1:800,13,replace=F)
>     geneCluster <- geneUniverse[geneCluster]
>     print(i)
>     print(geneCluster)
>     params <- new("KEGGHyperGParams", geneIds = geneCluster,
>           universeGeneIds = geneUniverse, annotation = "YEAST",
>            pvalueCutoff = 0.1, testDirection = "over")
>     hgOver <- hyperGTest(params)
>     dfrm <- summary(hgOver)
>     #print(dfrm)
> }
> 
> --------------------------------------------------------------------------------------------------------
> 
> The output/error that I got is:
> 
> [1] 1
>  [1] "YKR067W" "MOF9"    "YDR518W" "YPR074C" "YCL011C" "YCR069W" "YDL104C" "YGR136W" "YAR003W" "YFR013W" "YOR116C" "YDR507C" "YGR167W"
> [1] 2
>  [1] "YJR112W" "CEN8"    "YPL005W" "YHR081W" "YLR323C" "YBR131W" "YLR347C" "YHR098C" "YOR107W" "YCL027W" "YNR012W" "CRL16"   "YLR329W"
> [1] 3
>  [1] "YNL327W" "YEL056W" "YNL321W" "YDL111C" "YMR284W" "YLR338W" "YPL008W" "CRL17"   "YEL065W" "YFR027W" "YMR269W" "YPL019C" "YML038C"
> Error in numW - numWdrawn : non-numeric argument to binary operator
> 
> 
> [[elided trailing spam]]
> 
> My sessionInfo():
> 
>> sessionInfo()
> R version 2.6.2 (2008-02-08) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     
> other attached packages:
>  [1] KEGG_2.0.1          GOstats_2.4.0       Category_2.4.0      genefilter_1.16.0   survival_2.34       RBGL_1.14.0         GO.db_2.0.2        
>  [8] graph_1.16.1        goTools_1.10.0      annotate_1.16.1     xtable_1.5-2        AnnotationDbi_1.0.6 RSQLite_0.6-8       DBI_0.2-4          
> [15] Biobase_1.16.3      GO_2.0.1            hu6800_2.0.1        hgu95a_2.0.1        hgu95av2_2.0.1      hgu133plus2_2.0.1   hgu133b_2.0.1      
> [22] hgu133a_2.0.1       som_0.3-4           YEAST_2.0.1         cluster_1.11.10    
> 
> 
> thanks!
> 
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org