Is any prompt error message produced?
I'm not a Cytoscape expert, but I have found that in some cases if a
given edge attribute (column) has both numeric and letter values eg:
Node1 Node2 1.0
Node1 Node3 NA
Node1 Node4 2.3
The column is not read at all, or some fields remain empty. In general
I fix the problem replacing the 'NA' by something like '0.0' or
another numeric value that I can easily distinguish from "true"
numeric values -e.g. for colouring purposes-.
Also have occurred me that if I use decimals in only some fields, e.g:
Node1 Node2 1.0
Node1 Node3 5
Node1 Node3 2.3
I need to complete the '5' to '5.0' in order to take all the columns,
otherwise the attribute for pair 'Node1 Node3' appears empty (no
value).
Perhaps check is your matrix have something like this.
Javier.