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Infinium/Illumina 450K methylation array data analysis: How to compare the various packages/pipelines?
1
Entering edit mode
21 months ago
India

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?

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Entering edit mode
13 months ago
Freiburg, Germany

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.

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Entering edit mode
13 months ago
Duarte, CA

I have a template for comparing those algorithms here:

http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip

with relevant description here: http://www.nature.com/protocolexchange/protocols/2965

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.

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