Question: How to compute average methylation among multiple sites given raw sequencing reads
0
zhourudy20 wrote:

I have a question regarding calculating average methylation across all sites from one single gene. I have the raw data from chip bis sequencing in the following form.

15, 5,0.33

20,5,0.4

10,5,05

My question is since the total number of reads at different sites is different, which would be a better way to compute average methylation?

1. Take the ratio and divide by number of site?

2. Take the sum of #of C reads among all sites/ sum of Total reads?

I am leaning towards method #2 since I feel like its a more accurate depiction of the raw data but I wanna hear some opinions!

Thanks!

methylation chip-seq R • 1.6k views
modified 10 months ago by feljpants0 • written 4.9 years ago by zhourudy20

there is a typo - the second column should be 20,5,0.25

1
Devon Ryan94k wrote:

It's probably best to just take the weighted average. So for this "gene", you'd get:

`0.33*(15/(15+20+10)) + 0.4*(20/(15+20+10)) + 0.5*(10/(15+20+10))`

which is ~`0.399`.

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feljpants0 wrote:

the simple average and the weighted average output the same methylation percentage

18/45 = 0.33(15/(15+20+10)) + 0.4(20/(15+20+10)) + 0.5*(10/(15+20+10))