Prepare report for meeting

[halasadi]

We need to provide a summary of our progress to Matthew. We plan to present the following:

(1) What is the problem we are tackling? What have previous studies done and what are their flaws.

(2) Exploratory data analysis on the data : PCA and general Admixture

(3) (a) Talk about the basic model without sampling correction. We simulated under the WF model. Show the drift factor and how it's not a problem. (b) Show him how finite sample size can introduce a lot of error. (c) Show the real data analysis.

(4) We've developed a modification and show him the doc that we've prepared.

(5) (a) Under the new model, show results under simulations with and without drift. (b) Furthermore, apply the new model on real data.

(6) Main conclusions: We provide an alternate analysis to analyze ancient DNA. Our analysis shows that moderns cannot be written as a mixture of three source frequencies as claimed by Haak et al.

Discussion: drift and contamination.

[kkdey]

1). What is the problem we are tackling? What have previous studies done and what are their flaws

See : https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/introduction.pdf

2). Exploratory data analysis on the data : PCA and general Admixture

See : https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/plot_exploratory.pdf

3a). Talk about the basic model without sampling correction.

See: https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/model_1.pdf

3b). We simulated under the WF model. Show the drift factor and how it's not a problem. Show how finite sample size can introduce a lot of error.

See : http://htmlpreview.github.com/?https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/example_sim_drift_old.html

3c). Show the real data analysis

See: http://htmlpreview.github.com/?https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/Haak_data_analysis_model_1.html

4). We've developed a modification and show the doc that we've prepared.

See : https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/model_2.pdf

5a). Under the new model, show results under simulations with and without drift and talk about sampling correction

See: https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/example_sim_drift_new.pdf

5b). Apply the new model to the Haak Human Origins data

See: http://htmlpreview.github.com/?https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/Haak_data_analysis_model_2.html

6). Discussions

See: http://htmlpreview.github.com/?https://github.com/halasadi/ancient-structure/blob/master/docs/Matthew%20report/discussion.html