How-to: combinations of covariates using Ruby

I work with people who generate a lot of microarray data. One question that they often ask is: can we find those genes with a two-fold or more change in median expression under two or more different conditions?

For example, let’s say that we have 3 conditions: “normal”, “adenoma” and “cancer”. That gives us 3 pairwise comparisons: normal-adenoma, normal-cancer and adenoma-cancer. Here’s a Ruby solution to the problem.

RSRuby and Rails revisited

A couple of months ago, I wrote a brief guide to displaying R plots in a Rails application using RSRuby.

It worked at the time – really it did – but since then, I’ve encountered problems. One is that despite sending the plot output to a PNG file, R X11 windows started to pop up on loading the web page containing the plot. Another is the appearance of long error messages related to “stack smashing” on terminating Mongrel server.

Fortunately, I read an excellent guide by Ana Nelson, R on Rails with RSRuby, which convinced me that I was doing things all wrong. So here is an amended version of my R + RSRuby + Rails “Hello World” application.

Where to share?

A brief and unscientific survey of social bookmarking buttons provided by journal websites. Take with pinch of salt and/or tongue in cheek.

PLoS get it. As you'd expect.	BMC get it too.	Even ACS kind of get it.
OUP get it to a degree.	Someone doesn't get it.

I know, all bookmarking services provide their own tools, such as bookmarklets. However, I suspect that a button is more convenient for many people: it’s a courtesy and an advertisement for social bookmarking and online reference management tools.

So NPG: is it “we promote sharing” or “we promote sharing so long as you use our service?”

Great work, ISMB microblogging team

Another year, another ISMB/ECCB meeting and – another great blogging effort.

It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too.

Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up.

How-to: search across linked tables using acts_as_ferret

I’m in the process of adding search to a Rails application, using acts_as_ferret and ran into this issue. How to search a table using a field from another table, supplied by a foreign key?