In documentation (beadsummary.pdf) of beadarray package it explains how to get a ExpressionSetIllumina from data deposited on GEO. Something like:
library(GEOquery)
url <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE33126/"
filenm <- "GSE33126_series_matrix.txt.gz"
if(!file.exists("GSE33126_series_matrix.txt.gz")) download.file(paste(url, filenm, sep=""), paste0(getwd(),'/',filenm))
gse <- getGEO(filename=filenm)
# Convert into ExpresssionSetIllumina:
summaryData <- as(gse, "ExpressionSetIllumina")
summaryData
However, this is already normalized data.
It also explains how to get "ExpressionSetIllumina"
from IDAT
files, but the raw data I am trying to get is not idat file, as you see in suppl. files of following studies:
GSE22247
GSE26677
I can get those supplementary txt files with:
dataRAW <- read.delim(paste0(txtpath), sep='\t', skip = 4, header = T)
How can I convert dataframe (dataRAW) into an ExpressionSetIllumina
object ?
p.s: I need raw data to test different normalisations and latter do dif. gene expression analysis.