We are now half-way through day one of APBC.
So far it has been fun.
Association mapping tutorial
The day started with tutorials. Four tutorials in two tracks. For the first tutorial, we attended Matthew Stephens’ tutorial on Bayesian and imputation methods for association mapping.
It was a very nice tutorial. He started out with presenting the general setup in a genome wide association study — so nothing new here for us — and then talked about Bayesian approaches and the benefit of using those.
Mainly motivated by the problem that a p-value does not tell you anything about the probability of there being no association — which is what you are probably interested in knowing — and does not capture uncertainty in the data caused by sample size of minor allele frequency. Well, in some way it does, since the power depends on sample size and MAF, but under the null model all p-values are equally likely, so the p-value in itself does not tell you about the probability of the null model being true.
In the Bayesian setup, you can calculate the probability of the null being true, the false discovery rate, fdr = P(null-model | data), from the posterior odds, PO = P(alternative-model | data) / P(null-model | data), since fdr = 1/(1+PO).
The posterior odds, of course, depends on the Bayes’ factor and the prior odds, but makes it easy to explicitly quantify the belief that the posterior or alternative model is the true model.
He spent a lot of time on ways of testing single markers for association in this framework, so very little time was left for multi-locus methods — which he skipped — and imputation methods — covered very quickly.
While I would have preferred to hear more about the last two topics, I still very much enjoyed the tutorial.
Off for coffee
In the break between tutorials Besenbacher and I talked imputation with Matthew, so we missed the beginning of the next tutorial session and decided to skip the next tutorial and instead the three of us went for coffee in a nearby Starbucks and continue our association mapping discussion.
The afternoon program started with a keynote talk by David Lipman on the molecular evolution of Influenza.
I’m personally very fascinated by influenza, especially because of the global pandemics it has caused, so this was a very interesting talk for me.
The last part of the afternoon is the first session with paper presentations, but the jet lag is kicking in and that — combined with the high temperature in the lecture hall — makes it hard to stay awake.
We’ve decided to skip this session and rest a bit, so we are ready for the reception in the evening.
13-15 = -2