Beta values (β) are the estimate of methylation level using the ratio of intensities between methylated and unmethylated alleles. β are between 0 and 1 with 0 being unmethylated and 1 fully methylated.
Now when compare values of a probe form 2 different sample, how to compare if methylated or unmethylated . As for example,
probe sample_A Sample_B cg_1 0.6 0.7 cg_2 0.2 0.3 cg_3 0.8 0.9 cg_4 0.2 0.9 cg_5 0.3 0.6 cg_6 0.1 0.4
Now how to compare a specific probe if methylated or not.
Some assumption :
- If a specific value ( 0.5) define methylated (greater than 0.5) or unmethylated (less than 0.5) state.
- If it is reasonable to measure the change ( difference) of beta values. For cg_6 difference is 0.3 (0.4-0.1), though the maximum value is less than 0.5.
- Or if consider both situation together.
May be the issue is really simple. But i am a bit unclear regarding this issue. I am expecting some expert's thinking on this issue.
Partly related : Interpreting Fractional Methylation Data