I have been given a methylation data set with a range of beta and M values and . I am very new to this and I am wondering what the best way would be to analyse both the Beta values between two groups of people (disease/control). What would be the best way to present this data (Bar graph/scatter plot?)
Also if possible, could someone explain why you would need to look at the variance or do an F-test?
Analyzing methylation data is a non-trivial task, so the best way to proceed would be to find a local statistician with experience who could help you. Failing that, you will need to educate yourself. A good place to start would be the minfi vignette. Unfortunately it appears to still be under construction, so you may need to read what's there, and then scroll down to the bottom to find the underlying references. Another useful resource is the methylation workflow. Maybe you should start there first.
But do note that this site is primarily intended to help people with specific questions about Bioconductor packages, rather than as a tutorial site for helping people with their analyses. Bioconductor packages are free in the sense that you can install and use them without paying any cash. But nothing is really free, and you have to pay by putting in the time to learn about the methylation platform, the statistical analysis you will be making, and R/Bioconductor. This is not cheap! If you have the time and inclination to learn all that stuff, then it's worth it. But if you don't, I would highly recommend finding someone who has already learned it and pay for their expertise.
