R help - Nov 2012 - fold change calculation

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?

Thanks so much


Vittoria

-- 

Vittoria Roncalli

Graduate Research Assistant
Center Békésy Laboratory of Neurobiology
Pacific Biosciences Research Center
University of Hawaii at Manoa
1993 East-West Road
Honolulu, HI 96822 USA

Tel: 808-4695693

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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