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bobthecat/getting_some_data.r

Created December 20, 2012 18:19
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getting_some_data.r
library(GEOquery)
## Download the data from GEO
GDS3716 <- getGEO('GDS3716')
# transform the GDS to and expressionSet
eset <- GDS2eSet(GDS3716,do.log2=TRUE)
phenoData <- pData(eset)
# keep only the ER+ and ER-
samples <- phenoData$sample[grep("ER", phenoData$specimen)]
# subsetting the expressionSet
eset <- eset[,samples]
# transforming to matrix
e <- exprs(eset)
# For the sake of the example here we keep only the first 2000 probes.
e <- e[1:2000,samples]
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