R/diagnostics_CompareOriginal.R

In Syksy/curatedTools: Tools for generating open multi-omics datasets with curated clinical data

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# Teemu Daniel Laajala
# Examine GEX profiles of re-processed files through raw files obtained from GEO
# Compare to the original gene expression profiles provided by the authors
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setwd("D:\\Postdoc\\curatedProstateData\\curatedProstateData_RAW")
load("GEX_Barwick.RData")
load("GEX_Sun.RData")
load("GEX_Taylor.RData")

# Use GEOquery to retrieve the data matrices
library(GEOquery)
# Barwick: GSE18655
GEO_GEX_Barwick <- getGEO('GSE2553',GSEMatrix=TRUE)
# Sun: GSE25136
GEO_GEX_Sun <- getGEO('GSE25136',GSEMatrix=TRUE)
# Taylor: GSE21032
GEO_GEX_Taylor <- getGEO('GSE21032',GSEMatrix=TRUE)