[R] fold change calculation

[David Winsemius]

On Nov 17, 2012, at 9:55 AM, Vittoria Roncalli wrote:

> Hi,
> I am really new to edge R and I have used it to calculate gene  
> expression
> with RNASeq data comparing 2 different conditions.
> I used a P value of 0.05 and I got a list of DGE contigs up and down
> regulated.
> WhatI was wondering is how to convert the logFC value that appear in  
> the
> output of the exact test.
> Is it a log2 base? Is fold 2 change considered as cutoff?
> I am trying to find this info on the manual but apparently I am not  
> able.
> Could someone help me?

I suspect you should be posing this question to the BioConductor  
mailing list. You really ought to include more information about what  
packages you are using and preferably include analysis code and enough  
code to construct an example.

-- 

David Winsemius, MD
Alameda, CA, USA