I'm trying a pagerank analysis in FELLA (R code and input data are attached) and I'm getting an error message.
When I try:
enrich(..., method = 'pagerank', approx = "simulation", niter=10000)
I'm getting:
Running PageRank...
Estimating p-values by simulation.
Using pagerank matrix. Damping factor will be the one with which the database was built
Error in double(n.nodes) : object 'n.nodes' not found
In addition: Warning message:
In defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground, :
Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
Copied original message from Ben: Hi Sergio,
I'm trying a pagerank analysis in FELLA (R code and input data are attached) and I'm getting an error message.
When I try: enrich(..., method = 'pagerank', approx = "simulation", niter=10000)
I'm getting: Running PageRank... Estimating p-values by simulation. Using pagerank matrix. Damping factor will be the one with which the database was built Error in double(n.nodes) : object 'n.nodes' not found In addition: Warning message: In defineCompounds(compounds = compounds, compoundsBackground = compoundsBackground, : Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.