ssizeRNA: Sample Size Calculation for RNA-Seq Experimental Design

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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")'.

Author
Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Date of publication
2016-10-22 12:17:42
Maintainer
Ran Bi <biran@iastate.edu>
License
GPL (>= 2)
Version
1.2.8

View on CRAN

Man pages

check.power
Average Power and True FDR Based on limma/voom RNAseq...
hammer.eset
RNA-seq data from Hammer, P. et al., 2010
sim.counts
RNA-seq Count Data Simulation from Negative-Binomial...
ssizeRNA_single
Sample Size Calculations for Two-Sample RNA-seq Experiments...
ssizeRNA_vary
Sample Size Calculations for Two-Sample RNA-seq Experiments...
ssize.twoSampVaryDelta
Sample Size Calculations for Two-Sample Microarray...

Files in this package

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