[BioC] total number of reads? mapped reads? or total counts?

[Mark Robinson]

Hi Shan,

We typically use a fourth concept, the notion of 'effective' library size.

The idea is quite simple, and spelled out here:
http://genomebiology.com/2010/11/3/R25

And, the function is implemented in edgeR's calcNormFactors().

HTH,
Mark

On 12.12.2011, at 17:44, wang peter wrote:

> hello all
> 
> 
> In the edgeR package，
>  the lib.size: vector of length ncol(counts) giving the total number
> of reads sequenced
> for each sample. If not separately provided, will be set to colSums(counts).
> 
> but there are three different concepts.
> 
> usually the number of mapped reads < total reads < counts
> because not all of the reads can be mapped
> and one mapped reads have more than 1 hit.
> 
> so which one should be used in the NB model?
> 
> -- 
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
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