[BioC] power calculation of RNA-Seq

[Wu, Hao]

Yanzhu,

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.

Regards,
Hao





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.



Best,


Yanzhu








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

vignette("PROPER")

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>
http://www.stat.brown.edu/zwu


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.



Best,


Yanzhu




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


Best,


Yanzhu




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