Dowload data from GEO with GEOquery (short note)

download_with_geoquery.R

library(GEOquery)

# Get GSE
gse <- getGEO("GSE147507",GSEMatrix=FALSE)
head(Meta(gse))

# names of all the GSM objects contained in the GSE
names(GSMList(gse))

# and get the first GSM object on the list
GSMList(gse)[[1]]

# and the names of the GPLs represented
names(GPLList(gse))

# Download GSE as an expressionSet
gse <- getGEO('GSE147507',GSEMatrix=TRUE)
show(gse)
class(gse[[1]])
class(gse[[2]])
# This GSE entry consists of 2 expression sets
head(pData(gse[[1]])) # Human dataset
head(pData(gse[[2]])) # Ferret dataset