Download GEO datasets with GEOquery

GEOquery_download.R

library(GEOquery)

# Download existing RA datasets

# Study 1
# Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S et al. Transcriptome 
# analysis describing new immunity and defense genes in peripheral blood 
# mononuclear cells of rheumatoid arthritis patients. 
# PLoS One 2009 Aug 27;4(8):e6803. PMID: 19710928
# Reference: 	GSE15573

# Download GSE15573
gse <- getGEO("GSE15573")
class(gse)
show(gse)
show(pData(phenoData(gse[[1]]))[1:4,])
class(gse[[1]])

# The expression set is a first element of the list 
eset <- gse[[1]]
head(pData(eset))
class(eset)
# Save expression set
save( eset, file="GSE15573_ESet.RData" )

# Save the expression matrix
write.csv(exprs(eset), file="GSE15573_expressions.csv")

# Get sample data
write.csv(pData(eset), file="GSE15573_phenodata.csv")

# Get annotation
gpl <- getGEO(eset@annotation)
class(gpl)
head(gpl@dataTable@table)
annotation <- gpl@dataTable@table
head(annotation)[1:3,]
# Save annotation
write.csv(annotation, file="GSE15573_annotation.csv")