ssizeRNA: Sample Size Calculation for RNA-Seq Experimental Design

We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.

Install the latest version of this package by entering the following in R:
install.packages("ssizeRNA")
AuthorRan Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Bioconductor views DNASeq DifferentialExpression ExperimentalDesign GeneExpression Microarray RNASeq Sequencing
Date of publication2017-01-09 10:00:34
MaintainerRan Bi <biran@iastate.edu>
LicenseGPL (>= 2)
Version1.2.9

View on CRAN

Files

inst
inst/NEWS.txt
inst/doc
inst/doc/ssizeRNA.R
inst/doc/ssizeRNA.Rnw
inst/doc/ssizeRNA.pdf
NAMESPACE
data
data/hammer.eset.RData
R
R/sim.counts.R R/ssizeRNA_vary.R R/ssize.twoSampVaryDelta.R R/ssizeRNA_single.R R/check.power.R
vignettes
vignettes/ssizeRNA_ref.bib
vignettes/ssizeRNA.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/check.power.Rd man/ssizeRNA_vary.Rd man/hammer.eset.Rd man/ssizeRNA_single.Rd man/ssize.twoSampVaryDelta.Rd man/sim.counts.Rd

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