Hi, I am a edgeR user and I am a little bit confused on the normalization
topic.
I am using EdgeR to get different expressed genes within 3 conditions
(RnaSeq) with 3 replicates each.
I am following the user guide step:

-update counts file (from mapping against reference transcriptome)
- filter the low counts reads (1cpm)
- reassess library size
- estimate common dispersion

Mi first question is related to the normalization. Why, after I import my
file, next to the library size there is then column with norm.factors?

$samples

                 group lib.size norm.factors

X48h_C_r1.sam  CONTROL 10898526            1

X48h_C_r2.sam  CONTROL  7176817            1

X48h_C_r3.sam  CONTROL  9511875            1

X48h_LD_r1.sam      LD 11350347            1

X48h_LD_r2.sam      LD 14836541            1

X48h_LD_r3.sam      LD 12635344            1

X48h_HD_r1.sam      HD 11840963            1

X48h_HD_r2.sam      HD 17335549            1

X48h_HD_r3.sam      HD 10274526            1



Is the normalization automated? What is the difference with the
"calNormFactors?"

Moreover, if I do not run the calNormFactors, what is into the
pseudo.counts output?


I am very confused about those points.


Thanks in advance for your help.


Looking forward to hearing from you.


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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