Apply Hidden Markov Model (Hmm) On Tiling Array

Question

[Sandeep]

Hi All,

I am currently working on the analysis of Agilent 244k CpG island array to estimate methylation. I want to apply HMM to the fold change values of each probe to identify regions of contiguous probes with similar fold change.

Can anyone please suggest a way to achieve the same?

Thank you

Answer 1

[Sean Davis]

You can probably apply any of the CGH-type packages (aCGH, biohmm, or even CBS), at least mechanically, but I doubt this will get you useful results. I think the analysis of high-resolution methylation array data is still an area of active research.

[Sandeep]

Thank you Sean for the reply. I was looking at "http://www.sciencedirect.com/science/article/pii/S0888754309002675". They have applied HMM to their probes using Partek GS. BioHMM might just work. Will try it for now.