DNA methylation analysis package "Minfi"

Question

[soyeon]

Hi ,

I'm studying about minfi package.

I don't understand the bisulfite conversion results. And beta-value,M-value too.

How should I interpret the data for the figure?

enter image description here

Answer 1

[Basti]

This plot aims to compare the intensity values of bisulphite conversion control probes. It is an important step in quality control check. From one sample to another, the intensity of the probes should not differ too much. If you check your green and red dots patterns, it seems two samples differ from the others. You should be aware that these samples might not be of high quality and you should investigate the possible causes that led to this.