Testing code in RMarkdown documents with knitr


Over the last few months, Literate Programming  has proved to be a huge help to me in documenting my exploratory code in R. Writing Rmarkdown documents and building them with knitr not only provides me a greater opportunity to clarify my code in plain English, it also allows me to rationalise why I did something […]


Posted by on July 1, 2017

Using Packrat with Bioconductor in RStudio


As an R programmer, you may not be familiar with the development processes involved in programming Java. For those of you who have written some production Java code, you may have found that the barrier to entry can seem quite high. With so many tools you need to grok in order to have a basic […]


Posted by on June 5, 2017

Bioconductor Tip: Use affycoretools to get Gene Symbols for your ExpressionSet


For whatever reason, following on from my despair with normalizing gene expression data from earlier in the week, my most recent challenge has been to take a Bioconductor ExpressionSet of gene expression data measured using an Affymetrix GeneChip® Human Transcriptome Array 2.0 but instead of labeling each row with its probe ID having it mapped […]


Posted by on March 25, 2017

Be pragmatic about your choice of laptop in Bioinformatics


Recently I have been familiarising myself with analysing microarray data in R.  Statistics and Analysis for Microarrays Using R and Bioconductor by Sorin Draghici is proving to be indispensible in guiding me through retrieving microarray data from the Gene Expression Omnibus (GEO), performing typical quality control on samples and  normalizing expression data over multiple samples. As an […]


Posted by on March 18, 2017

Converting nginx access logs to tsv using bash


To my humble satisfaction, Gwasanaethau Cymru (Services Wales) was launched a mere week and a half ago. It is my first genuine effort to write a publically accessible web application that I intend to actively maintain so that I can grow my Java development skills. I have nginx web server sitting in front of my […]


Using Vagrant to test Apache Spark applications


Apache Spark is fast becoming the established platform for developing big data applications both in batch processing and, more recently, processing real-time data with the use of Spark streaming. For me, Apache Spark really shines in that it allows you to write applications to run on a Yarn Hadoop cluster and there is little to […]


R XML Package


I’ve spent a number of years programming in Java so, during my MSc in Bioinformatics, it took me a while to become acquainted with the nuances and the idioms of writing code in R. It has been discussed extensively elsewhere, little better than John Cook’s lecture R: The Good, The Bad and The Ugly. While […]


Posted by on August 12, 2016

Personal project success


With a glut of free time of late, I have chosen to take some time to write some code as part of a personal project. Primarily, I wanted to really dive deeply into Spring framework beyond the basics of web application development. At the same time I didn’t want the effort to go to waste […]


Posted by on August 7, 2016