Network generation error and input file format

[Shrikirti Anand]

Hi... I want to create a network of 15 genes which I have entered as source node and 201 other genes which I have entered as target node. The issue is that the 15 genes which I have entered as source is just creating a network with the first 15 genes of the target that too, one on one, serially . The rest of the genes of the target  node are forming a cluster in itself. I am attaching a picture so that it is more clear to you guys. Also I have entered the input data in csv format. My operating system is windows 10.

[Scooter Morris]

Hi Shrikirti,

I think you're over-interpreting the "Source Node" and "Target Node" columns.  Each row in the CSV represents an edge, so if you have two source nodes where each node connects to 4 target nodes, you would need 8 rows:

source1 target1

source1 target2

source1 target3

source1 target4

source2 target1

source2 target2

source2 target3

source2 target4

We have to do things that way because most networks are sparse -- that is, not all source nodes connect to all target nodes.

-- scooter