Author Archives: Mike

Backing up to USB with a batch Script in Microsoft Windows

I have recently reentered the world of work and have been issued with a brand new computer that has Windows 10 on it. In years passed, I developed an aversion to using Windows and was frustrated at each institution that … Continue reading

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Unsubscribe from all your YouTube channels with one weird trick

Here’s a short one for you. I have wanted to clear my list of subscribed channels in YouTube for a long time. Unfortunately, it seems that in recent years, there’s no automated way of doing this. If, like me you … Continue reading

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Calculate average ranking in R

Here is short post to describe how to calculate the average rank from a set of multiple ranks listed in different data.frames in R. This is a fairly straightforward procedure, however, it took me more time than I anticipated to … Continue reading

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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 … Continue reading

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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 … Continue reading

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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 … Continue reading

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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), … Continue reading

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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 … Continue reading

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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 … Continue reading

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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, … Continue reading

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