Hi,
I am using edgeR to detect differential expression in NGS experiments.
I have a brief question on what I should considered as "total size of my 
libraries".
In my case I have a set of samples that have a quite large variation  in 
the library size:

Total reads Mapped reads

1 11076283 8736308

2 5881045 4006468

3 7139703 5108608

4 9089153 5643701

5 9723103 8457914

6 15570265 8706332

7 15844448 12056310

8 13375681 8663496

9 14997114 8799752

10 15744584 8555922

11 4642056 3201515

12 6458028 4277204

13 13206724 9466118

14 3035032 2148730


Should I insert as lib.size parameter the values referring to the real 
size of the libraries (Total reads) or
simply the size of the mapped reads (Mapped reads)

Thanks for the help
Raffaele

-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero@unito.it
        raffaele[dot]calogero[at]gmail[dot]com
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Info: http://publicationslist.org/raffaele.calogero


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