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It is very common to cluster genes based on their expression profiles, and also very common to integrate Gene Ontology to observe the distribution of biological processes, molecular functions and cellular components for a given gene list. But, what if the two in combination? The Gene Ontology distributions across a ... [Read more...]

Hadley Wickham has just announced the release of a new R package “reshape2” which is (as Hadley wrote) “a reboot of the reshape package”. Alongside, Hadley announced the release of plyr 1.2.1 (now faster and with support to parallel computation!). Both releases are exciting due to a significant speed increase they ... [Read more...]

As prolific as the CRAN website is of packages, there are several packages to R that succeeds in standing out for their wide spread use (and quality), Hadley Wickhams ggplot2 and plyr are two such packages. And today (through twitter) Hadley has updates the rest of us with the news: ... [Read more...]

It’s common knowledge that I struggle wrapping my head around the apply functions in R. That is illustrated very clearly in the following discussion on Stack Overflow: Dirk’s comment is actually spot on. I’ve asked the same damn question at least 4-5 times. Only I didn’t ... [Read more...]

United Nations report World Population Prospects: The 2008 Revision (highlights available here) provides data about the historical and forecasted population of the country. In exploring the future and past population trends it is relatively easy to subset the dataset by your selected variable. __ file population names(population) [Read more...]

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Although the graphic at the left might not seem a 100% appropriate, it gives a hint to what I am about to do. I want to calculate all possible linear regression models with one dependent and several independent variables. I do not want to address bias and fitting issues or the ... [Read more...]

Today I will treat a problem I encounter every once in a while. Let’s suppose we have several dataframes or vectors of unequel length but with partly matching column names,  just like the following ones: df1 [Read more...]