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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