BackgroundThis tutorial shows an example of RNA-seq data analysis with DESeq2, followed by KEGG pathway analysis using GAGE. Using data from GSE37704, with processed data available on Figshare DOI: 10.6084/m9.figshare.1601975. This dataset has six samples from GSE37704, where expression was quantified by either: (A) mapping to to GRCh38 using ... [Read more...]

This short post will explore a funny dataset that forms part of R’s dataset library. The dataset will loaded out of interest of its content as well as using it to enagage with Hadley Wickhams’s ggplot2 package. The dataset that will be used to expl... [Read more...]

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The regular monthly upstream Armadillo update gave us the second update in the 6.* series: version 6.300.2. This was rolled into RcppArmadillo 0.6.300.2 which was once again tested against all reverse-dependencies before being sent to CRAN and Debian where the new packages arrived yesterday. Besides the changes by Conrad, this version of RcppArmadillo ... [Read more...]

World Development Indicators After my last post on deaths from assault, I got a few comments both on and off-line asking for exploration of developing country issues, in contrast to the OECD focus of the previous post. I’d always intended at some point to do something with the World ... [Read more...]

Web Scraping to Item Response Theory: A College Football Adventure Brandon LeBeau, Andrew Zieffler, and Kyle Nickodem University of Iowa & University of Minnesota Background Began after Tim Brewster was fired Wanted to try to predict next great coach Data Available Data is available at three levels Coach Game by Game ... [Read more...]

A new minor release of RQuantLib was released onto CRAN and into Debian. It takes advantages of some changes from last week's QuantLib release 1.7. Particularly noteworthy is the addition of support for intra-daily times in QuantLib based on work by... [Read more...]

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by Joseph Rickert If there is anything that experienced machine learning practitioners are likely to agree on, it would be the importance of careful and thoughtful feature engineering. The judicious selection of which predictor variables to include in a model often has a more beneficial effect on overall classifier performance ... [Read more...]

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I’ve prepared a short console-based data-driven R game named ,,The Proton Game’’. The goal of a player is to infiltrate Slawomir Pietraszko’s account on a Proton server. To do this, you have to solve four data-based puzzles. The game can be played by beginners as well as heavy ... [Read more...]

Up until a few weeks ago I would style my code like this: I thought that was the only way… until I witnessed a DBA friend of mine coding. He would write the same function like this: In my opinion, the second style makes the code easier to read. I ... [Read more...]

The 16th Cologne R user group meeting is scheduled for this Friday, 4 December 2015 and we have great line up with three talks followed by networking drinks. Monitoring process change using Bayesian methods (Mick Cooney) A common business problem is to... [Read more...]

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OVA and AVA? Huh? These stand for One vs. All and All vs. All, in classification problems with more than 2 classes. To illustrate the idea, I’ll use the UCI Vertebral Column data and Letter Recognition Data, and analyze them using my regtools package. As some of you know, I’... [Read more...]

Following on yesterday's announcement of RcppCCTZ, what is the only thing better than another date, time, or timezones library package? One that works on Solaris too :) Bradley White from CCTZ upstream spotted the failed compilation on the machine in Oxford and suggested a quick fix. Jeroen quickly tested what I ... [Read more...]

There are three functions available in the tigris package (https://github.com/walkerke/tigris) to fetch road data. primary_roads() loads all interstates for the entire US; primary_secondary_roads() gets you interstates and US/state/county highways, by state; and roads() gets you all road segments for a given ... [Read more...]

There are three functions available in the tigris package (https://github.com/walkerke/tigris) to fetch road data. primary_roads() loads all interstates for the entire US; primary_secondary_roads() gets you interstates and US/state/county highways, by state; and roads() gets you all road segments for a given ... [Read more...]