hammer.eset

RNA-seq data structured as an expressionSet, from "mRNA-seq with 
agnostic splice site discovery for nervous system transcriptomics tested in 
chronic pain" by Hammer, P. et al. (Genome Res. 2010, 20(6):847-860), 
tools:::Rd_expr_doi("10.1101/gr.101204.109").


datasets


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")'.

Ran Bi

ssizeRNA

Sample Size Calculation for RNA-Seq Experimental Design

Peng Liu

Tim Triche

hammer.eset function

Ran Bi <a href="/link/biranpier%40gmail.com?package=ssizeRNA&version=1.3.3" data-mini-rdoc="ssizeRNA::biranpier@gmail.com">biranpier@gmail.com</a>, Peng Liu <a href="/link/pliu%40iastate.edu?package=ssizeRNA&version=1.3.3" data-mini-rdoc="ssizeRNA::pliu@iastate.edu">pliu@iastate.edu</a>

Author

RNA-seq data from Hammer, P. et al., 2010 — hammer.eset

Ran Bi <a href='mailto:biranpier@gmail.com'>biranpier@gmail.com</a>, Peng Liu <a href='mailto:pliu@iastate.edu'>pliu@iastate.edu</a>

hammer.eset: RNA-seq data from Hammer, P. et al., 2010

Description

Usage

Arguments

Value

Author