If it's not too much Trouble, can someone tell me as to how do I, read in the txt file in R studio? The Raw data was downloaded from GEO. The data accession number is GSE48624.

Moreover, how do i Differentiate the control sample from the normal sample since there are only txt files available in the raw data compressed file!

Thank you very much!

The "raw data" for this dataset seem to be the annotation files for the arrays, and not the raw intensities at all. So not helpful for analysis.

However, you can use the GEOquery package to import the normalised intensities

library(GEOquery)
remotefile <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48624/matrix/GSE48624_series_matrix.txt.gz"

destfile <- "GSE48624_series_matrix.txt.gz"
if(!file.exists(destfile)) download.file(remotefile, destfile)
mydata<- getGEO(filename=destfile)

Phenotypical data can be obtained using the pData function

pd <- pData(mydata)

pd

The vector pd$source_name_ch1 will tell you whether each sample was in the before or after group

pd$source_name_ch1

The function exprs will extract the normalised values

exprs(mydata)

Hope this helps,