[BioC] DEGraph graph format?

[Dan Tenenbaum]

I'm CC'ing the maintainer of DEGraph...
Dan


On Thu, Jun 7, 2012 at 5:43 PM, Hamid Bolouri <hbolouri at fhcrc.org> wrote:
> 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
>
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