[BioC] how to get normalized counts from edgeR

[Mark Robinson]

Hi Shan,

On 09.07.2012, at 05:05, wang peter wrote:

> dear all:
> i have two questions
> 
> 1. is the "size factor" from DESeq equally to the "norm factor" in the edgeR

No.  In edgeR, the library size and additional normalization scaling factors are separated.  See the two different columns in the $samples element of a 'DGEList' object:

> d$samples
         group lib.size norm.factors
sample.1     1    12367    0.9746280
sample.2     1    12088    1.0243994
sample.3     2    12823    0.9897893
sample.4     2    12374    1.0119267


In all the downstream code, the lib.size and norm.factors are multiplied together to act as the effective library size; this (product) would be similar to DESeq's size factor.


> 2. i can get the normalized counts by
> 
> counts(obj,normalized=T)
> 
> how to get normalized counts from edgeR
> can i use the each col of count matrix divided by norm factor


In edgeR, you can use cpm().  For example:

  d <- DGEList(counts=...)
  nc <- cpm(d, normalized.lib.sizes=FALSE)

You might have a skim through the edgeR user's guide; many of these concepts are described in more detail there.

Best,
Mark



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