[BioC] power calculation of RNA-Seq

Wu, Hao hao.wu at emory.edu
Thu Sep 11 21:32:03 CEST 2014


Not sure whether Zhijin has answered. But unfortunately at this time, PROER only works for two-group comparison. Developing power calculation for general experimental design is on our todo list. Sorry we can't be more helpful for your data.


From: Yanzhu Lin <mlinyzh at gmail.com<mailto:mlinyzh at gmail.com>>
Date: Wednesday, September 10, 2014 2:40 PM
To: Zhijin Wu <zwu at stat.brown.edu<mailto:zwu at stat.brown.edu>>
Cc: "bioconductor at r-project.org<mailto:bioconductor at r-project.org>" <bioconductor at r-project.org<mailto:bioconductor at r-project.org>>, "Wu, Hao" <hao.wu at emory.edu<mailto:hao.wu at emory.edu>>
Subject: Re: power calculation of RNA-Seq

Hi Professor Wu,

I have successfully loaded the vignette and have taken look at it, but I am still not clear how to use the package for my project. The following is some information about my project.

My project has a multi-factor design, which includes three factors: L with 16 levels, S with 2 levels and E with 3 levels, hence it ends up with  16 x 2 x 3 = 96 groups. There are 8 biological replicates within each group. We already have our RNA-Seq read count data available.

I would like to test how much power we have for 8 biological replicate per group based on the RNA-seq read count data we have.

BTW, in the vignette of PROPER, I didn't find the function works for mulit-factor design, do you mind telling me where I can find the functions work for multi-factor design? Thanks.



On Wed, Sep 10, 2014 at 10:50 AM, Zhijin Wu <zwu at stat.brown.edu<mailto:zwu at stat.brown.edu>> wrote:
Hi Yanzhu,
  The vignette (software manual) is distributed with the PROPER package. Examples with code are given for various situations in the vignette. Just type


in R (after you load the package) and it should open up the pdf file.

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

Tel: 401 863 1230<tel:401%20863%201230>
Fax: 401 863 9182<tel:401%20863%209182>

On 9/10/2014 9:21 AM, Yanzhu Lin wrote:
Hi Dr. Wu,

I am very interested in the package of power calculation of RNA-Seq data
with factorial design mentioned in your post and I would like to try it. I
have downloaded the package from the link you provided. But, I am not clear
how to use it, could you give me an example about how to use it?

Your help will be greatly appreciated.



On Tue, Jul 1, 2014 at 9:58 AM, Michael Love<michaelisaiahlove at gmail.com<mailto:michaelisaiahlove at gmail.com>>

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:


On Tue, Jul 1, 2014 at 9:53 AM, Yanzhu Lin<mlinyzh at gmail.com<mailto: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.



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