Monthly Archives: August 2011

Dataset in Public

Posted by on August 31, 2011 3 comments

I get requests from time to time about sharing my Reference 3 dataset. I use a few datasets which I am not allowed to redistribute, but most of the others are actually public and the main issue is to convert them to plink format and merge them.

I have released code for the conversion already but to make the task even easier I am letting you guys know that I already released a subset of my dataset a long time ago. Razib wrote about it and added the detailed instructions on using that dataset.

So here's the link to the dataset which contains about 30,000 SNPs and almost 4,000 individuals from HapMap, HGDP, SGVP, Behar et al and Xing et al.

Related Reading:

Ugly's Electrical References, 2011 Edition
Public Enemy Zero
Merriam-Webster's Everyday Language Reference Set
The Foolish Dictionary An exhausting work of reference to un-certain English words, their origin, meaning, legitimate and illegitimate use, confused by a few pictures [not included]
Legends of the middle ages, narrated with special reference to literature and art

Admixture Ref3 Dendrogram HRP0001-HRP0160

Posted by on August 12, 2011 42 comments

I haven't done any admixture dendrograms in a while, so I thought you guys might be interested.

This uses admixture results using Reference 3. As usual, I used complete linkage for the hierarchical clustering.

Let's look at the dendrogram using regular Euclidean distance measure between admixture results.

I also decided to use chi squared distance measure to do the clustering.

PS. Any thoughts on the trees based on two different distance measures?

Related Reading:

Ancient Cities of the Indus Valley Civilization
Script of Harappa & Mohenjodaro & Its Connection With Other Scripts
Mathematical Tools for Data Mining: Set Theory, Partial Orders, Combinatorics (Advanced Information and Knowledge Processing)
Algorithms of the Intelligent Web

Admixture (Ref3 K=11) HRP0151-HRP0160

Posted by on August 9, 2011 10 comments

Here are the admixture results using Reference 3 for Harappa participants HRP0151 to HRP0160.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

There are several interesting participants here. HRP0151 is a quarter Nepalese and his/her results are actually quite odd. The East Asian ancestry shows up as Native American which is possible. I wonder if the quarter Chinese ancestry is not Han but rather some other Chinese ethnicity.

HRP0155 is Sri Lankan Sinhalese and has a lower Onge component than I expected.

HRP0158 is my Dad and has similar results as me (HRP0001).

Related Reading:

The Family Tree Problem Solver: Tried-and-True Tactics for Tracing Elusive Ancestors
Script of Harappa & Mohenjodaro & Its Connection With Other Scripts
The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry

23andme $50 Off

Posted by on August 2, 2011 6 comments

I got an email from 23andme for a $50 off coupon. The coupon code is YCM48E. So you can use this coupon code to reduce the price of a 23andme test from $99 to $49.

Here's the email:

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Get your friends and family on board with this $50 coupon. Share it with as many people as you like, but remember that this coupon expires in 7 days (August 9, 2011).

Have fun!

The 23andMe Team

To use this coupon, visit our online store and add an order to your cart. Click "I have a discount code" and enter the code below.

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Coupon code: YCM48E

Share with your friends!

(Valid for new customers only)

Again the coupon code is YCM48E for $50 off till August 9, 2011.

Related Reading:

Discount Armageddon: An InCryptid Novel (Incryptid Novels)
The Creative Destruction of Medicine: How the Digital Revolution Will Create Better Health Care
Discount 3-Pack (Volume 2) [Sci-fi/Fantasy stories: "The Immortals of Penthouse 8", "Goodbye, Cruel World", and "Captain Peterpin's Trip to the Sun"]
Genes, Chromosomes, and Disease: From Simple Traits, to Complex Traits, to Personalized Medicine (FT Press Science)
Discount 3-Pack (Volume 1) [Scifi/Fantasy stories: "Bluebirds and Dead Canaries", "Uniform", and "Big Business"]