I am interested in looking at differentially methylated regions between 2 cell lines and a normal tissue of interest using publicly available data.
The data for the cell lines is available in the form of the raw IDAT files which I am thinking of processing using R to get the beta values. The data for the normal tissue is available in the form of Beta values. Both are from the GEO database. As I am unsure how the data for the normal tissue has been normalized, is it accurate to compare the data between them? If yes, how should I normalise the cell line data?
I am thinking of using the minfi package on R for the data processing of the cell lines but unsure what would be suitable to then identify the differentially methylated regions. Would appreciate any advice and help as I am an undergraduate with basic bioinformatics background. Thank you!
