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Is There A Way To Get The Single Best Model From A Group Of Models/States Generated By Chromhmm?

Hi!

Is their a way to get the single best model from a group of models/states generated by ChromHMM?

Thank you

chip-seq
• 3,820 views • link
updated by Ram Ram • written by Dataminer Dataminer

you can decide arbitrarily as long as you can make sense of the number of chromatin states that you see.

• 82 views • link
written by biorepine biorepine

Hi, sorry for an old thread, but did you ever figure out how to do this? I am thinking of using BIC because most papers using ChromHMM end up using BIC to score their models and pick the best one. I do have a question about the "size" of my observed data though.

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written by Affan Affan

1 answer

I'm going to point you to an answer I wrote to a similar question on CrossValidated: http://stats.stackexchange.com/a/126343/61963

The linked answer is more detailed, but the short version of the answer is: BIC/AIC are not good methods to select the best model in this case, and the only good model is the one that you can interpret biologically (by cross-referencing with secondary annotations like TSSs, enhancers, etc).

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updated by Ram Ram • written by Matt Corley • Matt Corley

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