General questions concerning mathylation analysis

Question

[Hashirama]

Dear community,

I got some methylation data back from the sequencing facility and I wonder how to work with them as there are different formats.

I have 1.) scanner data as .idat file 2.) Raw, not normalized, data as tab separated text or .csv 3.) Quantile normalized expression values as .csv

What data should I take to do the calculations? Could you please recommend some R packages to perform the analysis? Another problem is that each data file is > 20 GB big... Is it okay to work in R environment with such large files?

Thank you very much!

Answer 1

[jared.andrews07]

You likely want to work from the IDATs. See this vignette for an example workflow.

IDATs are not that large and you can likely handle many (i.e. 100s of samples) locally even with modest resources.