Download GEO files using R and GEOquery

source("http://bioconductor.org/biocLite.R") # download BioC installation routines
biocLite() # install the core packages
biocLite("GEOquery") # install the GEO libraries

library(GEOquery)
getGEOSuppFiles('GSE20987')
untar("GSE20987/GSE20987_RAW.tar", exdir="data")
cel_files <- list.files("data/", pattern = "gz")
cel_files_qualified <- paste("data", cel_files, sep="/")
sapply(cel_files_qualified, gunzip)