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.htm l 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

Hi Michael, Great. Actually, I have sent an email to the author of RNASeqPower R package asking whether the package can take care of multi-factor design. Best, Yanzhu On Tue, Jul 1, 2014 at 9:58 AM, Michael Love <michaelisaiahlove@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.h tml > > > On Tue, Jul 1, 2014 at 9:53 AM, Yanzhu Lin <mlinyzh@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]]

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.h tml > > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor