From GEO omnibus I have download raw intensities from a 450k methylation array (in a tab-delimited text format). However, there are duplicates of some of the probes:
example for Sample 1:
There are two rows for this probe, one for Address A and one for Address B:
- cg00000622 (Address = 11642304)
- cg00000622 (Address = 38691301)
However, each has a methylated and an unmethylated intensity
- methylated = 907 unmethylated = 10835
- methylated = 120 unmethylated = 735
How do I get this down to single methylated and unmethylated values for this probe? (so that I may calculate the beta value).
Is this a type I probe or is one of them a control probe?
Thanks for any help