Berger paper

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I apologize for not getting to this yesterday, but I just checked the Berger et al. (2010) reference, and it seems to be fine. I used the DOI and got right to the page, but here's the direct link: http://www.pnas.org/content/107/41/E157.

In case you don't know what DOIs are or how to use them, here's a brief explanation:

"DOI" stands for "digital object identifier", a system

for identifying content objects in the digital environment. DOI® names are assigned to any entity for use on digital networks. They are used to provide current information, including where they (or information about them) can be found on the Internet. Information about a digital object may change over time, including where to find it, but its DOI name will not change. (from http://www.doi.org/)
The Berger et al. reference looks like this in the notes:

James Berger, Stephen Fienberg, Adrian Raftery, and Christian Robert.
Incoherent phylogeographic inference.
Proceedings of the National Academy of Sciences USA, 107(41):E157-E157, 2010.
10.1073/pnas.1008762107.
That last line is a DOI. To use it to get the paper simply put type the following URL into the address bar of your favorite browser:

http://dx.doi.org/10.1073/pnas.1008762107

http://dx.doi.org is the URL of the database that keeps track of DOIs. To find a specific DOI, you simply type the DOI at the end of that URL (after a "/") and it will take you there.

Final set of notes posted

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I made the final set of changes to my notes on approximate Bayesian computation and uploaded them a few minutes ago. You'll find them in the link for today's lecture. I'll also add them to the outline of notes as soon as I finish typing this entry. Now that I've finished them, it seems pretty clear that I won't have more than a few minutes to say anything about next generation sequencing, but I've added links to several papers where you can find more information on what sorts of things may be possible and the challenges to making those possibilities real.

On a different note, please remember that you should send me your answer to Problem #7 no later than 5:00pm next Wednesday, 15 December. I guarantee that I'll get every paper graded, meaning I can assign final letter grades, if I get your paper by then. If I don't get it by then, I might be able to get it graded in time to turn in something other than an incomplete, but I can't make any promises.

Study Sessions for Problem 5

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Hi all,

I'm waiting for final confirmation but tentatively the study sessions will be the following:

Wednesday Nov 10 from 1-5

Tuesday Nov 16 from 11-2

I don't have a lot of free time other than those slots, so PLEASE try to bring your questions to at least one of them!

Cheers
Kathryn

UPDATE: I have a doc apt on Wed, so I will be gone from 2-3.  Sorry!

Expectation for Friday Class

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Hi all,

The goal for Friday's class is to make sure everyone knows the following:

1)  How to run R
2)  How to get the output of R into a format you can actually use
3)  How to use GenBank

In order to accomplish this goal, please download R, the data file and the "key to SNPs" file before coming to class.  Saving all of these on your desktop will also make life easier.

If you already know how achieve the above mentioned goals, feel free to take the day off.

One final thing: Please think about when you would like me to hold a study session for this problem.  I'd really like to only hold one!

Cheers
Kathryn

Preview of association mapping

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The issue of Nature that just came out happens to have a bunch of articles relevant to association mapping, which we'll start talking about on Monday. The report on the 1000 genomes project, the accompanying review by Rasmus Nielsen, and the overview of human association mapping by Monya Baker are particularly relevant. If you have a chance, you may find it helpful to glance at them before Monday.

Solution to Problem #3

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Kathryn typed up her answer to Problem #3. I've converted it to a PDF and posted it. Feel free to contact either of us with questions about it.

Expectations for Problem 4

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Hello everyone!

Just so that we are all clear, since Problem 4 is a "larger" problem, I am expecting essentially "results" paragraphs for questions 1 & 2 and a page-long "discussion" for question 3, as well as the code for solving the problem.

I'd recommend reading the paper associated with the problem if you haven't already!

Cheers
Kathryn

Exponents in WinBugs/OpenBugs

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Hi all,

I've gotten a couple of questions so I thought I'd let you all know how to code for an exponent in WinBugs/OpenBugs.

Let's say you want to raise 10 to the power of 2 (ie 10 squared).

Rather than using 10^2 which is what Excel has drilled into our brains, you type
pow(10, 2) 
where pow is the "power" function, 10 is the factor and 2 is the exponent.

If we change the situation and decide that we want to raise (1-x) to the power of 2 we can do this 2 ways:

pow ((1-x), 2)

OR

y<- 1-x
pow (y, 2)

However, WinBugs/OpenBugs won't actually let you do a power function the first way, so you'll have to use the second notation.  Remember that x and y can be anything you want them to be (since they are just symbols) so make sure they match the rest of your code!

Hope this helps!

Kathryn

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wsd_eng_thumb.png
You might be interested to know that today is World Statistics Day. Just what you wanted, right? A whole day to celebrate statistics.

Updates

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I've uploaded a new version of Problem #4 It includes the two corrections I mentioned in lecture this morning.

  1. I've corrected the formula for Var(pt).
  2. I've corrected a couple of entries in the table of data.
I've also uploaded a commentary on Problem #2 that Kathryn put together.