questions on HotNet web server input

[bioliyezhang]

Hi,
I wonder whether anyone has experience with HotNet, (http://ccmbweb.ccv.brown.edu/cgi-bin...cgi/upload.php)

I tried to use its online (web) version, but I have several questions regarding to the input for the program, can someone help me with it?
Thanks a lot.

I want to ask few simple questions about running Hotnet on the server.
Let's say, I am studying lung cancer, and I have 10 samples.
I know what to put for the mutations_file, CNA_file

for the length files
Question 1: we just provide the length of the mature mRNA, right?

for the tested_file
Question 2: what do I provide in here? Should I provide the
genes known to be related to lung cancer? or what?

for the BMR:
Question 3: what should I put here, if I use the background
mutation rate is 4 per Mb?

for the delta:
Question 4: do you have a suggested delta to start with?
Question 5: if I want to run the program to find the
threshold, what num_rep and num_threshold do you suggest?

for the num_rep:
Question 6: what do you suggest to use if I am running the Hotnet?

Best,
Liye