Hi Hao, Thank you very much for letting me know, I really appreciate it. Best, Yanzhu On Thu, Sep 11, 2014 at 3:32 PM, Wu, Hao <hao.wu at="" emory.edu=""> wrote: > 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=""> > Date: Wednesday, September 10, 2014 2:40 PM > To: Zhijin Wu <zwu at="" stat.brown.edu=""> > Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">, "Wu, Hao" < > 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=""> 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 >> Fax: 401 863 9182 >> 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="">>> > >>> 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/RNASeqPowe r.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 >>>>> >>>> >>>> >>> > [[alternative HTML version deleted]]