[BioC] SPIA

[Martin [guest]]

So my question is, why can't I integrate 
hsa03030.xml,hsa03410.xml,hsa03420.xml,hsa03430.xml,hsa03440.xml
hsa03450.xml,hsa04520.xml
in the SPIA hsaSPIA.RData file?

makeSPIAdata(kgml.path=mydir,organism="hsa",out.path="./")
[1] TRUE

But if I run
spia(de=diff_exp,all=all_exp,organism="hsa",data.dir="./",nB=2000,plots=FALSE,beta=NULL,combine="fisher",verbose=FALSE)

the pathways don't exist in the table.

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] SPIA_2.15.2      KEGGgraph_1.14.0 graph_1.36.2     XML_3.95-0.1    

loaded via a namespace (and not attached):
[1] BiocGenerics_0.4.0 stats4_2.15.2      tools_2.15.2   

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