[BioC] how to set library size in DESeq?

[Simon Anders]

On 02/15/2012 04:24 AM, wang peter wrote:
> how to set library size in DESeq?
> i know how to set library size in edgeR
> d<- DGEList(counts = d, lib.size =
> c(9893630,11055814,11207084,9663487,11455088,8140053), group =
> group)#生成DGEList对象
> but donot know how to set library size in DESeq
> it seems i can set size factor
> 
> sizeFactors(object)<- value or pData(cds)$sizeFactor<- value
> but how to set library size？
> 
The size factor is all there is to set.

For the analysis, the algorithm only needs to know the size of a library
_relative_ to the other libraries. The total library size is irrelevant.

In edgeR, the information is split over two field, one with the library
sizes, and one with normalization factors. If you multiply the library
sizes with the normalization factors (and divide by some constant to get
values close to one), you get edgeR's equivalent to DESeq's size
factors, and (to my knowledge) this is all that edgeR uses internally.

Why would you want to set the library size?

  Simon