Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).
This R script performs automated differential analysis from Illumina's expression idat files. By default this script assumes idat files are from HT12 V4 arrays, but with little modification it should work with any arrays.
Make sure you have the following dependencies installed:
beadarray, illuminaHumanv4.db, limma, ggplot2, ggrepel
###Usage:
Clone this repo and source analyzeBead.R
Arguments:
idats = input IDAT files
names = Sample names for each idat file
condition = Sample conditions for each idat file
ref.condition = reference condition.
fdr = FDR cutoff. Default 0.05
pltPCA = If TRUE performs PCA
#Example usage with four idat files (2 control and 2 treated).
source("AnalyzeBead.R")
bead.results = beadAnalyze(idats = c("file1.idat","file2.idat","file3.idat","file4.idat"),
names = c("control1","control2","treated1","treated2"),
condition = c("control","control","treated","treated"),
ref.condition = "treated",
fdr = 0.05, plotPCA = T)