Recently I tried compiling Eigensoft on my Ubuntu 10.10 Linux system running in Virtualbox and had no success. From comments on this blog post, it looks like the newer Ubuntu distros don't have the libg2c0 and related libraries (which were a part of the gcc3) and gcc4 uses gfortran instead.

This builds on a previous post from Stephen.I was recently running a series of ANOVA analyses, and I used the aov() function because it had a few options that I preferred. Much like lm(), the function returns an object that you typically pass to summary() to view and interpret the output. It took me a bit of playing to figure out how to extract the information I needed.

After finishing the final revisions on my dissertation I was reminded of this spot-on graphical guide to what a Ph.D. is really all about. Now that I'm finished, I'm leaving Vanderbilt to start a postdoc in genetic epidemiology with Dr. Loic Le Marchand at the University of Hawaii Cancer Center. Posts may be sparse over the next few weeks, but I plan on blogging as usual once I'm set up at my postdoc.

I thought it would be trivial to extract the p-value on the F-test of a linear regression model (testing the null hypothesis R²=0). If I fit the linear model: fit<-lm(y~x1+x2), I can't seem to find it in names(fit) or summary(fit). But summary(fit)$fstatistic does give you the F statistic, and both degrees of freedom, so I wrote this function to quickly pull out the p-value from this F-test on a lm object, and added it to my R profile.

Coming from the lineage of Jason Moore, I am obliged to occasionally remind everyone that biological systems are inherently complex, and to some degree, we should therefore expect statistical models involving those systems to be complex as well. With the development of GWAS, many approaches to examine epistasis are weighed down by the computational burden of exhaustively conducting billions of statistical tests.

When I started grad school I started using Reference Manager (RefMan), similar to EndNote, to manage my references and bibliographies. It's a real pain, and I often feel like I'm powering my computer with the endless pumping and clicking of the mouse that it takes to import a reference into my library. Recently I've started using Zotero because of how easy it is to import references, store PDFs, and sync between computers.

About a year ago I wrote a post about Dropbox - a free, awesome, cross-platform utility that syncs files across multiple computers and securely backs up your files online. Dropbox is indispensable in my own workflow. I store all my R code, perl scripts, and working manuscripts in my Dropbox. You can also share folders on your computer with other Dropbox users, which makes coauthoring a paper and sharing manuscript files a trivial task.

R evangelist David Smith, marketing VP at Revolution R, will be giving a webinar showing off some of the finer features of Revolution R Enterprise - an integrated development environment (IDE) for R that has an enhanced script editor with syntax highlighting, function completion, suntax checking, mouseover help, R code snippets for common tasks, an object browser, a real debugger, and more. Revolution R Enterprise is free for academics.

I was recently reading a bit about logistic regression in Gelman and Hill's book on hierarchical/multilevel modeling when I first learned about the "divide by 4 rule" for quickly interpreting coefficients in a logistic regression model in terms of the predicted probabilities of the outcome. The idea is pretty simple.

While preparing for my upcoming defense, I found a cool little web app called pubmed2wordle that turns a pubmed query into a word cloud using text from the titles and abstracts returned by the query. Here are the results for a pubmed query for me ("turner sd AND vanderbilt"): And quite different results for where I'm planning to do my postdoc: Looks useful to quickly get a sense of what other people work on.

On Friday, December 3rd, at 8:00 AM, after copious amounts of coffee, my friend, colleague, and perpetual workout buddy Stephen Turner will defend his thesis. Join us in room 206 of the Preston Research Building at Vanderbilt Medical Center for the auspicious occasion!Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.