I want to normalize the Illumina Infinium methylation microarray data by lima, or by minfi or other programs you would recommend.
The online available GEO... has: *family.soft data, matrix file, and RAW data like: v1.1.bpm, v1.2.bpm, *.csv, manifest/header_descripton.xls. and RAW data with: TargetID Proband393_mother.Signal_A Proband393_mother.Signal_B Proband393_mother.Detection Pval Proband393_father.Signal_A Proband393_father.Signal_B Proband393_father.Detection Pval and so on....
I checked the lumi tutorial and the package required IDAT data.
Could anyone tell me what data should I use to the normalization? I want to get the Methylation fractions (of Beta value) and the genomic locations of them.
I would be very grateful for help. I am new in epigenetics and still learning.