[BioC] Heatmap hints and identifying differentially expressed genes

[Steve Lianoglou]

Hi,

> Here is another quick question: how do I calculate the p-value for  
> each
> gene? I'm simply calculating the fold-changes. But it is better to do
> some kinds of statistical analysis. In my experiment, each sample  
> group
> is in triplicate. What is the best way to pick up differentially
> expressed genes (not using fold changes)?

Yeah, just fixing a global threshold of fold change for differential  
expression isn't really the best. For a relatively easy way to get  
differentially expressed genes, look into the limma package:

http://www.bioconductor.org/packages/2.3/bioc/html/limma.html

It'll get you the p-values you're after, as well.

Hope that helps,

-steve

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

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