This is the second time that I am writing about my learning experience from Earl F. Glynn at Stowers Institute. Unfortunately, it is not maintained since Oct. 2008. Well, I learned a lot from Earl, and would like to give my thankfulness to this website. Still, this is a good website about Gaussian property

With the current bimodal project, I have listed out a few important components and maybe plan to tackle the project.

Plotting histogram and overlap with fitting

Fitting different models to data

Get mixed models working

Get Bayesian’s models working

Extract parameters from models

This paper was published on
Journal of Statistical Planning and Inference in 2009.

The major data source was from the Old Faithful.

Here, I am reading and documenting papers and documents that help me to learn mixture model.

I have tried a Biomodal approach with another post I had earlier.

• MixtureModel 101
• EMnotes_001
• EMnotes_002

It seems that this write up EM4Beginners gives a good general description on the basic modeling, EM algorithm, MLE procedures, and even uses mixture distribution as an example.

Here is another good presentation on EM and supplemental materials are here

A good EM implementation example in R

Try to get this HMM implemented to handle the methylSeq DMR calls.

Major work flow

	
Load in DEG lists

	
Run common analysis, there are six major analysis




	
Core analysis

	
Tox analysis

	
Metabolomic analysis

	
Biomarker filter

	
Filter dataset

	
microRNA target filter




	
Other analysis

When I was working on Mehmet’s miRNA data (from Affymetrix miRNA-3.0 array), I encountered an error. It turns out that I need to install new library to read in .cdf platform.

source("http://bioconductor.org/biocLite.R")
biocLite("pd.mirna.3.0")

With miRBase mysql local set up, I can easily search for miRs. i.e.

 select * from mirna_mature where mature_name like "mmu-miR-15b%" ; 
+-------------+----------------+--------------------+--------------+--------------+-----------------------------------------------------------------------------------+------------+
| auto_mature | mature_name    | previous_mature_id | mature_acc   | evidence     | experiment                                                                        | similarity |
+-------------+----------------+--------------------+--------------+--------------+-----------------------------------------------------------------------------------+------------+
|       75243 | mmu-miR-15b-3p | mmu-miR-15b*       | MIMAT0004521 | experimental | cloned [17604727], Solexa [20215419,20413612]                                     |            | 
|       75242 | mmu-miR-15b-5p | mmu-miR-15b        | MIMAT0000124 | experimental | cloned [12007417,12919684,15538371,16766679,17604727], Solexa [20215419,20413612] |            | 
+-------------+----------------+--------------------+--------------+--------------+-----------------------------------------------------------------------------------+------------+