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