[BioC] how to set library size in DESeq?

[Simon Anders]

Hi

On 02/15/2012 02:57 PM, wang peter wrote:
>          thank you very much for your clear explanation.
> i want to set the library size as the mapped read number.
> so i can define any one sample as one, and then
> others relative ratios. is it right to set the size factor?

I still do not know _why_ you would want to set the size factors. In a 
standard analysis, this should not be done. Rather you should use the 
estimators provided by the software (function 'estimateSizeFactors' in 
DESeq, or 'calcNormFactors' in edgeR). Unless you have very good reasons 
to believe that these functions do not work for your data, the results 
of your analysis will become worse if, instead of using them, you enter 
library sizes manually. See the paper by Oshlack and Robinson (and also 
ours on DESeq).

   Simon