Dear List, Thanks to Dan Bebber for pointing out a bug in the function ftM2graphNEL in the "graph" package and to Seth for help with fixing it. Those who use this function should update to version 1.12.1 in the release branch http://www.bioconductor.org/packages/1.9/bioc/html/graph.html or version 1.13.6 in the development branch. The bug is a lesson on "beware of partial matching when accessing list elements by name": x = list(foobar="lemon") x[["a"]] # NULL x[["f"]] # [1] "lemon" But x = list(foobar="lemon", f="plum") x[["f"]] # [1] "plum" and as a result, edges in the graph were invented if there were nodes with no out-edges whose name partially matched the name of other nodes with out-edges. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber