I am working on a GEO series methylation dataset (GSE) that I have downloaded from the GEO site. The downloads include three different files, 1) GSE_Matrix_methylated_signal_intensities.txt.gz 2) GSE_Matrix_methylated_signal_intensities.txt.gz 3) GSE_RAW.tar, since there is no IDAT file provided for this dataset I am looking to find a way to process the meth and unmeth files. Both the meth and unmeth files have raw intensities for each CpG across different samples, but it doesn't enlist the detection P-values for each CpG. Is there a way to process this data? In the past I have used minfi to do this, but I've always had the IDAT files.
I appreciate all help and comments.