[BioC] PreProcess and Limma 'done'. What directions now?

[Steve Lianoglou]

Hi Massimo,

On Jun 9, 2009, at 9:13 AM, Massimo Pinto wrote:

> Greetings BioC list readers,
>
> I have been working over the past few weeks on data normalization
> first (Agi4X44PreProcess) and linear models then (limma). I sense that
> I may have reached a point where questions may be addressed regarding
> regulation of individual genes of interest, as well as gene ontology.
>
> Would you please so kindly provide advice with regards to my next
> step? In brief, I would like to
>
> 1) Query expression of genes of my interest, which are known to be
> implicated in the biology that I am working on

I'm not sure what you're asking to do here, actually, since after  
doing your normalization/etc. this is the easy part, right?

You can just select these rows out of your normalized data matrix, or  
highlight their probe values on an MA plot, or plot their points on a  
pdf of your signal intensities. If you're looking for their  
differential expression calls, you'd just extract their +1/-1 calls  
post-limma-facto, if you will :-)

> 2) Get information about gene ontology

There are several package you can check. You've already mentioned  
goProfiles, but you might also want to consider GOstats as well.  
There's also topGO.

> 3) Ask about involvement of signaling pahways

I'm not sure about this one, but searching the bioconductor d/l page  
for the word "pathway" comes up with several leads, like SPIA and  
sigPathway.

I've never used either of these, but perhaps you can let us know how  
you like them :-)

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos