Infinium/Illumina 450K methylation array data analysis: How to compare the various packages/pipelines?

Question

[arpit.singh1203]

Hello

I am planning to work on 450K methylation array data. There are various pipelines/packages for data analysis. I don't need to know the best or the standard pipeline for the analysis. However I would appreciate ideas on how to compare various pipelines?

For a sample data I can use minfi, ChAMP, COHCAP, RnBeads and so forth. But how do I compare which one is working best for me?

Answer 1

[Devon Ryan]

In general, to see what algorithm is producing better results, you need to either (A) have a dataset with some known differences or (B) perform an independent validation of some of the discordant results produced by the various packages.

Answer 2

[Charles Warden]

I have a template for comparing those algorithms here with relevant description here.

One important limitation with the demo dataset is the small number of validated sites, but you can use the templates to get an idea of what the results would look like for your own data.