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")'. For R version 3.5 or greater, please use 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install("ssizeRNA")'.
| Version: | 1.3.3 |
| Depends: | R (≥ 3.2.3) |
| Imports: | MASS,Biobase,edgeR,limma,qvalue,ssize.fdr, graphics, stats |
| Suggests: | knitr |
| Published: | 2025-04-08 |
| DOI: | 10.32614/CRAN.package.ssizeRNA |
| Author: | Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb] |
| Maintainer: | Ran Bi <biranpier at gmail.com> |
| License: | GPL-2 |GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| In views: | ExperimentalDesign |
| CRAN checks: | ssizeRNA results |
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