[BioC] Normalization

[Ryan C. Thompson]

To answer your first question, when you first create a DGEList object, 
all the normalization factors are initially set to 1 by default. This 
is equivalent to no normalization. Once you use calcNormFactors, the 
normalization factors will be set appropriately.

I'm not sure about the second question. Could you provide an example of 
how you are obtaining pseudocounts with edgeR?

On Wed 27 Feb 2013 05:12:27 PM PST, Vittoria Roncalli wrote:
> 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
>
>
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