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Download GEO datasets with GEOquery
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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") | |
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