[BioC] DEGraph graph format?

[Hamid Bolouri]

hello;

Can anyone tell me how to use DEGraph with the pathways in NCIGraphData? 

The DEGraph Demo: 

>data("Loi2008_DEGraphVignette", package="DEGraph")
>classData <- classLoi2008
>exprData <- exprLoi2008
>annData <- annLoi2008
>grList <- grListKEGG
>res <- testOneGraph(grList[[1]],exprData,classData,verbose=T,prop=0.2)

works fine for me. But replacing grList with NCI.cyList from NCIGraph: 

>library(NCIgraphData)
>data("NCI-cyList")
> NCI.cyList[[1]]
A graphNEL graph with directed edges
Number of Nodes = 35 
Number of Edges = 40 

I get this error:

>res <- testOneGraph(NCI.cyList[[1]],exprData,classData,verbose=T,prop=0.2)
Keeping genes in the graph *and* the expression data set...
 35 genes of the graph were not found in the expression data set: 
  chr [1:35] "6749854621221256793-pid_m_25632-674985462-829166685-pid_m_100726" ...
 227 genes of the expression data set are absent from the graph: 
  chr [1:227] "31" "32" "207" "208" "355" "356" "369" "572" ...
Error: all.equal(dataGN, graphGN) is not TRUE
Keeping genes in the graph *and* the expression data set...done

I get the same error with 'reactome.cyList' graphs and with graphs generated by 'parseNCInetwork'.

Thanks

Hamid Bolouri

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] NCIgraphData_0.99.4 DEGraph_1.8.0       R.utils_1.12.1     
[4] R.oo_1.9.3          R.methodsS3_1.2.2  

loaded via a namespace (and not attached):
 [1] BiocGenerics_0.2.0 graph_1.34.0       grid_2.15.0        KEGGgraph_1.12.0  
 [5] lattice_0.20-6     mvtnorm_0.9-9992   NCIgraph_1.4.0     RBGL_1.32.0       
 [9] RCurl_1.91-1.1     RCytoscape_1.6.3   Rgraphviz_1.34.1   rrcov_1.3-01      
[13] stats4_2.15.0      tools_2.15.0       XML_3.9-4.1        XMLRPC_0.2-4