I have used bioconductor package FEM on my 450k methylation and RNAseq data. I followed the instruction described in the vignette. I can manage to run DoEpiMod and DoExpMod functions on the methylation and RNAseq datasets successfully independently. However, when I tried to run DoFEMbi on the same datasets, I got the following error:
It seems to process through the "Constructing weighted network" step successfully but fails at the "Running Spin-Glass algorithm" step. Any suggestions to overcome this error ? Thanks a lot.
 "Running Spin-Glass algorithm"
Error in .Call("R_igraph_spinglass_my_community", graph, weights, as.igraph.vs(graph, : At clustertool.cpp:472 : Cannot work with unconnected graph, Invalid value
Here is the code that I used:
intFEM.allProbe <- list(statM=statM.o.mval.dm, statR=statR.o.voom.de, adj=hprdAsigH.m) fembi.allProbe <- DoFEMbi(g1FEM.allProbe, nseeds=100,gamma=0.5,nMC=1000,sizeR.v=c(1,100), minsizeOUT=10,writeOUT=TRUE,nameSTUDY="g1-allProbe_fem",ew.v=NULL);