Hello Ryan,

Thanks very much for the clarification. It really helps.

Regards


On Thu, Jan 9, 2014 at 12:40 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote:

> 1) Is it fine to use both common and trended dispersion?
>>
>
> You can estimate both common and trended dispersions on the same DGEList
> object, but only one of them will be used. The other will be ignored. I
> believe that trended dispersion will always be preferred over common
> dispersion if both are available.
>
>
>  2) is there any specific conditions to use common or trended dispersion
>> estimation?
>>
>
> Well, broadly speaking, if you believe that there is a dependency between
> mean and dispersion in your data, then you need trended dispersion. If not,
> you would use common dispersion. A number of publications have argued that
> when modeling RNA-seq data with the negative binomial distribution, such a
> dependency exists. For example, the (I think) original DESeq paper:
> http://genomebiology.com/2010/11/10/R106/
>
> So generally you would always want to use trended dispersion if you are
> analyzing RNA-seq. For other types of data, you would likely want to test
> that assumption.
>
> -Ryan
>



-- 
Reema Singh
Postdoctoral Research Assistant
College of Life Sciences
University of Dundee,
Dundee DD1 4HN, Scotland
United Kingdom
http://www.compbio.dundee.ac.uk/people.html

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