[BioC] GOstats: HyperGTest for KEGG

[Marc Carlson]

Hi Paul,

It turns out that you are not doing anything wrong.  Regrettably, it
seems that you were just doing it at the wrong "time".  :P

I have just checked in a fix for this and it should be propagated
through the build system within a day or so. This bug only should have
affected the case where you are using KEGG, GOstats and the organism
package for yeast.  Please let me know if you have any other
difficulties and thank you for helping us to improve our code. 


  Marc




Paul Evans wrote:
> Hi,
>
> I was trying to get significant KEGG terms for yeast. Previously, I used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db" package. A sample of the code, and the error I get is reproduced below:
>
> ------------------------------------------------ Begin code -----------------------------------------------------------------
> ## TEST HYPERGTEST FOR KEGG
>
>  #library("YEAST")
>  library("org.Sc.sgd.db")
>  library("GOstats")
>  library("GO")
>
>
>   x <- org.Sc.sgdGENENAME
>   # Get the gene names that are mapped to an ORF identifier
>   mapped_genes <- mappedkeys(x)
>   # Convert to a list
>   xx <- as.list(x[mapped_genes])
>   if(length(xx) > 0) {
>     # Get the GENE NAME for the first five genes
>     xx[1:5]
>     # Get the first one
>     xx[[1]]
>   }
>
>  ## Create gene universe
>  geneUniverse <- allGenes[3000:4500]
>
>  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 = "org.Sc.sgd.db",
>             pvalueCutoff = 0.1, testDirection = "over")
>      hgOver <- hyperGTest(params)
>      dfrm <- summary(hgOver)
>  }
>
> -------------------------- End code --------------------------------------
>
> The error I get is:
>
> [1] 1
>  [1] "YJR004C" "YJL108C" "YJL188C" "YIL157C" "YKL039W" "YJR002W" "YIL139C"
>  [8] "YJR024C" "YIR021W" "YJR063W" "YJL166W" "YIR032C" "YKL049C"
> Error in get(paste(lib, name, sep = "")) : 
>   variable "org.Sc.sgdPATH2PROBE" was not found
>
>
> The GO enrichment analysis seems to work fine, it's just the KEGG that seems to cause problems. What am I doing wrong?
>
>
> thanks!
>
>
>
> PS: sessionInfo is:
>
>
>   
>> sessionInfo()
>>     
>
> R version 2.8.1 (2008-12-22) 
> 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 
> [8] methods   base     
>
> other attached packages:
>  [1] org.Sc.sgd.db_2.2.6  YEAST_1.16.0         cairoDevice_2.9-2   
>  [4] yeast2.db_2.2.5      gWidgetsRGtk2_0.0-48 GOstats_2.8.0       
>  [7] Category_2.8.2       genefilter_1.22.0    survival_2.34-1     
> [10] RBGL_1.18.0          goTools_1.16.0       PFAM.db_2.2.5       
> [13] KEGG.db_2.2.5        GO.db_2.2.5          org.Mm.eg.db_2.2.6  
> [16] org.Hs.eg.db_2.2.6   hgug4112a.db_2.2.5   hgug4110b.db_2.2.5  
> [19] hu6800.db_2.2.5      hgu95a.db_2.2.5      hgu95av2.db_2.2.5   
> [22] hgu133plus2.db_2.2.5 hgu133b.db_2.2.5     hgu133a.db_2.2.5    
> [25] RSQLite_0.7-1        DBI_0.2-4            som_0.3-4           
> [28] yeast.db0_2.2.5      cluster_1.11.12      Rgraphviz_1.14.1    
> [31] geneplotter_1.20.0   annotate_1.20.1      xtable_1.5-4        
> [34] AnnotationDbi_1.4.2  lattice_0.17-17      Biobase_2.2.1       
> [37] graph_1.20.0         gWidgets_0.0-32     
>
> loaded via a namespace (and not attached):
> [1] grid_2.8.1         GSEABase_1.4.0     KernSmooth_2.22-22 RColorBrewer_1.0-2
> [5] RGtk2_2.12.7       XML_1.94-0.1   
>
>
>
>
> -----------------------------------------------------------------------------------------------------------------
>
>
>
>
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