[BioC] Heatmap hints and identifying differentially expressed genes

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Mar 2 16:30:02 CET 2009


> 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:


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

Hope that helps,


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


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