[BioC] Tigre Question

[Antti Honkela]

Dear Anisha,

If you do not specify knownTargets, GPRankTargets() will just use the TF 
mRNA profile to fit the model of unobserved TF protein profile and 
target mRNA profile.

If you specify for example knownTargets=c('a', 'b', 'c'), 
GPRankTargets() will first fit a model to targets a, b, c to infer the 
TF protein profile. It will then augment this model with each candidate 
target one at a time, while keeping the parameters related to a, b, c 
fixed to essentially fix the protein profile. The use of TF mRNA profile 
in this mode is optional - it can help if it is informative about the 
active TF protein concentration, but it should not be used if the TF 
activity is mainly determined by some other factor, e.g. some 
post-translational modification.


Antti


On 2014-02-24 14:30 , Solanki, Anisha wrote:
> Dear Antti,
>
> Hope you are well. I had a question about the command GPRankTargets().
> It has an input knownTargets. How different would the command run if you
> specify some known targets compared to when you don't specify them.
> If you don't specify the targets how does the command screen for target
> genes. Does it only use the protein concentration predict from the mRNA
> Expression?
>
> Thanks
> Anisha

-- 
Antti Honkela
antti.honkela at hiit.fi   -   http://www.hiit.fi/u/ahonkela/