[BioC] runSPIA() in graphite package

[array chip]

Hi all, I am using runSPIA() from graphite package to analyze a gene list against biocarta pathway database. 


> library(graphite)

> prepareSPIA(biocarta, "biocartaEx")
> obj<-runSPIA(de=siggenes, all=allgenes, "biocartaEx")


where "siggenes" are a list of 1332 significant genes selected from "allgenes" (a list of 17138 genes). The running process verbose indicated a total of 178 pathways analyzed. 


One of the pathways I am particularly interested is "estrogen responsive protein efp controls cell cycle and breast tumors growth":

> p <- biocarta[["estrogen responsive protein efp controls cell cycle and breast tumors growth"]]
> nodes(p)
[1] "CDKs"             "Cyclin B1/2"      "EntrezGene:2099"  "EntrezGene:2810"  "EntrezGene:57154" "EntrezGene:7157"  "EntrezGene:7706"   "ubiquitin"

And my siggenes contains 2 of genes involved in this pathway:

> siggenes[c('7706','2099')]
     7706      2099 
 4.347012 -3.792425

So I would assume that runSPIA will examine this pathway during the  calculation, but surprisingly I didn't see this particular way being examined. Here is the section of runSPIA() verbose output that started with "e":

Done pathway 42 : e2f1 destruction pathway..
Done pathway 43 : effects of calcineurin in kera..
Done pathway 44 : egf signaling pathway..
Done pathway 45 : endocytotic role of ndk phosph..
Done pathway 46 : epo signaling pathway..
Done pathway 47 : erk and pi-3 kinase are necess..
Done pathway 48 : erk1/erk2 mapk signaling pathw..
Done pathway 49 : eukaryotic protein translation..
Done pathway 50 : extrinsic prothrombin activati..


Can anyone tell me why runSPIA() missed this pathway? Attached are siggenes and allgenes for you to try. 

> siggenes<-as.matrix(read.table("siggenes.txt",row.names=1))[,1]

> allgenes<-as.matrix(read.table("H:\\test\\allgenes.txt", row.names=NULL, header=T, colClasses='character'))[,1]

Many thanks

John
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