A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays

Draft of the manuscript A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays, developed as a package (see here). Note:

• Draft source is in vignettes, compiled draft is in inst/doc
  • Makes use of functions in R/
• Raw data is in inst/extdata, relevant R data files are in data
  • The preprocess function, when run within the main directory, turns the data in inst/extdata into the .rda files in data. The vignette (manuscript) makes use only of the .rda files built into the package
  • Some datasets have documentation, others don't yet but will

Installation

You'll first need to install the following packages:

source("http://bioconductor.org/biocLite.R")
biocLite(c("limma", "edgeR", "DESeq2", "org.Sc.sgd.db", "GO.db"))

install.packages("devtools")
devtools::install_github(c("dgrtwo/broom", "dgrtwo/biobroom", "dgrtwo/GSEAMA"))

Then open factorial.Rproj and under the Build tab, click "Build & Reload." It should install the remaining packages. You can then go to vignettes/factorial.Rnw and click Compile PDF.

To compile the supplemental material, go to vignettes/supplemental.Rnw and click Compile PDF again.

Deposited Data

The microarray data used in this experiment is available from the Gene Expression Omnibus (accession GSE65365), and the RNA-Seq reads are available from the NCBI Short Read Archive (BioProject accession PRJNA271248).