[BioC] power calculation of RNA-Seq

[Zhijin Wu]

We have a simulation based method and R package for RNA-seq power
calculation that includes factorial design. Our package includes two 
components: (1) a semi-parametric simulation that generates data based 
on actual RNA-seq experiments with flexible choices on baseline 
expressions, biological variations, patterns of DE (so if your 
collaborating biologists cannot fill in all the blanks for what you 
should assume, which is typically the case, you have very reasonable 
start by simply saying "I think it would resemble a typical cell line"); 
and (2) a power assessment component that provides a comprehensive view 
of power.

The package is currently available at
http://web1.sph.emory.edu/users/hwu30/PROPER.html, and will be submitted
to bioconductor very soon (Hao Wu is the developer but traveling). A 
manuscript is under review. Users are welcome to try out the package and 
we appreciate your feedback.


------------------------------------
Zhijin (Jean) Wu
Associate Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu

On 7/1/2014 9:58 AM, Michael Love wrote:
> Let's keep the discussion on the list. This provides a searchable
> archive for other Bioc users with similar questions.
>
> A google search for "bioconductor rna-seq power calculation" reveals:
>
> http://www.bioconductor.org/packages/release/bioc/html/RNASeqPower.html
>
>
> On Tue, Jul 1, 2014 at 9:53 AM, Yanzhu Lin<mlinyzh at gmail.com>  wrote:
>>
>> Hi Michael,
>>
>> Do you happenly know there is any package or paper works for power calculation of factorial design of RNA-Seq project? Thanks.
>>
>>
>> Best,
>>
>>
>> Yanzhu
>
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