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…

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…

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…

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…

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…