F_vs_K Plot on 'vsn-normalization.xls' -- Adding prior

Recovered Network (PDF) Threshold = 1.6

Recovered Network (PDF) Threshold = 3

Data: vsn-normalization.xls. ONLY Control network
Steps:
1. Adding 1 known connection as prior each time. Total is 10 tests, coming from 10 connections.
2. Retrain vbssm model and find optimal K value (10 retrainings all show k = 6 is the optimum)
3. Compare the recovered network with the known connections

Notes:
1." tdcF" and "tdcG" have *No* Entries in vsn-normalization.xls. Therefore, the following 4 intersections,

tdcA pp tdcF
tdcA pp tdcG
tdcR pp tdcF
tdcR pp tdcG

are excluded in the prior-test. There are 10 known connetions as prior candidates.
2. In CBDioZ, threshold = 1.6 / 3, consistent with that in the previous no-prior test.


------- Original Email --------------
Juan
I looked at your results. I see a few of the known connections in
top50®.sif in any of the reconstructed Control network. For instance,

tdcA pd tdcB
tdcA pd tdcC
tdcA pd tdcD
tdcA pd tdcE

are ok but the following are missing

tdcA pp tdcA
tdcA pp tdcF
tdcA pp tdcG


tdcR pp tdcA
tdcR pp tdcB
tdcR pp tdcC
tdcR pp tdcE
tdcR pp tdcF
tdcR pp tdcG
tdcR pp tdcD

You need to cross-check the .sif files carefully to see what is correct.

What I suggest is that we concentrate on the Control network for now, and start to add the known connections in top50&reg.sif as priors. You might want to do these 1 regulator at a time, and retrain the vbssm models. I guess you will need to repeat the F vs K plots first. What we ought to see is that known connections persist in the models.

By the way ihfAihfB pp tdcA should be

ihfA pp tdcA
ihfB pp tdcA

etc.

Please let me know if you have any questions about this.


Thanks

David

F_vs_K Plot on Vichy's Data

Vichy Data (70 genes) PDF

Linda,

Matrics File for vichy's data: yn.mat and inpn.mat

-Juan

-----------------------------------------------------------------
Linda

I looked at the plot and it looks fine.

The message below the plot suggests a matalb version problem. Can you
check if this is the problem?

You should now be able to proceed with producing a model for k =8 .

Maybe Juan has the matlab matrix file already and she can post it on the
website

David
-----------------------------------------------------------------------------------
Hi, David and Linda

This is the F vs K plot (10 seeds). k=8 is the optimum.

I had no trouble generating matrics (yn.mat and inpn.mat). I looked into the xls file and found from line 32 there are some notations following numerical data in the same row. I'm guessing the problem is probably coming from the function 'xlsread'. Is your MATLAB too old? I'm using MATLAB 7.0.1.

-Juan
--------------------------------------------------------------------------
Juan
Would you be able to help Linda debug this? I won't have any time to look
at it before next week. First key steps would be to produce F vs K plots
for this data. I don't un derstand what Linda means by "it would only
accept 31 out of the 70 genes".

Many thanks

David


---------- Forwarded message ----------
Date: Fri, 2 Mar 2007 17:05:25 -0000
From: "Hughes, Linda"
To: "'D.L.Wild@warwick.ac.uk' (E-mail)"
Cc: "B-Wollaston, Vicky"
Subject: modelling

Hi david

i ran vickys data through the modelling scripts. The bad news is that it
would only accept 31 of the 70 genes i wanted to put through to generate the
matrices. im not sure if this is a problem with the excel file or matlab as
i re-created the excel file a number of times but it still wont work.
i wonder if you could run the script with this excel file on your laptop so
i know where the problem is coming from.



<> <>

i decided to carry on with the 31 that would work and have run the FSvskk
script without any problem, heres a pdf of the output with a single seed (i
will put everything on the weblog when i come back) just ignore the control
data on the left. it seems that matrix 6 is the optimum.

<>

i was also wondering if you would send me a screen dump of the commands you
used to run CBDioZ after you loaded the relevant matrix for the example data
as being a newbie to matlab, im still struggling with syntax issues; im
particularly interested in the Imagesc command to view the interactions.
lastly im now connected to the buffalo servers and have been trying to run
theFSvskk script using the cluster, i was wondering if you new whether
matlab is installed on the server or whether i need to run it another way?
else i can just ask the buffalo people

sorry bout the long email, i just needed to ask everything before i go on
holiday and give you an idea of the current state of play

thanks

linda

Convert CBD matrix to Cytoscape Network

Linda,
common_gene_names.mat includes the gene names file convCyto_top50®.m reads.

load common_gene_names.mat

then the 56 genes(top50 & reg) names will show up.

> Please can you send Linda the gene names file that convCyto.m reads - in the example script it is '6reps_genenames_only.txt'? I guess you must have created this.

> David