[BioC] GeneNet

[Narinder Singh Sahni]

Dear Dr.Strimmer,

I have a question related to the use of bioconductor package GeneNet. According to the information provided
on the bioconductor download page " GeneTS has become a meta-package that exists mainly for 
reasons of backward compatibility. Its only purpose is to load the GeneCycle and GeneNet packages."

Neither GeneCycle nor GeneNet are amongst the list of packages supported by Bioconductor. Therefore,
I am routing this mail directly to you. You will hopefully have some time to answer my queries.

In the examples provided in the GeneNet and GeneCycle pakages, you have used a time course data
on a single treatment only (eg. the Arabidopsis data and the cell cyle data). I am on the other hand having
time course data for comparing two different treatments. There are a total of 9 time points (each replicated thrice), 
with time point zero common to both treatment groups (ie. there is no difference between trts. 1 and 2 at zero time
point). Thus, we have a total of 57 experiments.
 
Would it be correct to just combine the two treatments below each other as:
t1-1-1
t1-1-2
t1-1-3
t2-1-1
t2-1-2
t2-1-3 etc...
where t1-1-1 is read as trt 1 - time 1 - rep. 1.

1) Is there a more direct manner in which to define the two sets of treatments?

2)  Both the time series are unequally spaced and measured at 10 time points.
0, .5 , 1, 2 , 4,6,12,24,48, and 72 hrs.  time point 0 being common to both treatments. 
Does it make a difference in the final analysis if I convert these to coded values of 0,1,2,3,...9.
How can the time point zero which is common to both treatments be handled in this case.

Hopefully, this will not consume too much of your time. 

Thanking you for your assistance.

Sincerely,



Narinder Singh Sahni
Associate Professor
School of Information Technology
Jawaharlal Nehru University
New Delhi - 110067
India
Ph: +91-11-26704173
Fax: +91-11-26717586