lemieuxs

About Sébastien

Enjoys turning raw (big, noisy and convoluted!) biological data into knowledge… using any tools that informatics has to offer!

A javascript implementation of the non-central version of Fisher’s exact test

In a previous post, I presented a case for choosing a non-central version of Fisher's exact test for most of bioinformatics' uses of this test. I will now present an implementation of this test in javascript that could easily be embedded in web interfaces. Although javascript is probably the least likely language to implement statistical methods, I hope this article will fill in as many details as possible to make it trivial to port it to other languages if the need arises. At [...]

By | 2017-01-13T11:01:46+00:00 January 13, 2017|Categories: Javascript, Statistics, Test|0 Comments

The language(s) of bioinformatics

The most recurrent question I get regarding bioinformatics is unfortunately the one that leads to the least productive discussions I've participated in: Which programming language should I use for bioinformatics? Don't get me wrong, in a pub, over a beer, this can lead to some lively entertainment among the nerd intelligentsia... but rarely does it lead to enlightenment that persists in the morning! Here, I'd like to share the current answer I have honed over the past years. It is based [...]

By | 2016-11-08T09:30:05+00:00 April 18, 2016|Categories: Bioinformatics|0 Comments

Applying PCA to Leucegene data

GEO offers an extremely rich source of transcriptional profile data, but downloading and preparing a dataset is often an obstacle to aspiring bioinformaticians. I'll walk you through one way to do it using the Leucegene dataset as an example. Once this data is loaded and ready to use in R, I'll then present a very simplified and practical perspective on the use of PCA for exploratory analysis. Loading data A dataset of 285 transcriptional profiles of acute myeloid leukemia (AML) [...]

By | 2016-11-08T09:30:08+00:00 November 17, 2015|Categories: Data Analysis, R|0 Comments

Tweaking Fisher’s exact test for biology

Fisher's exact test is widely applied in bioinformatics (it is the core computation in gene-set or pathway enrichment analysis).  I won't introduce the test itself as others have done it several times (here), but will rather point to a disconnect between what it does and what is often needed. In Fisher's exact test, the null hypothesis is that there is no enrichment between the two variables studied.  When using this test with large numbers (such as the number of genes [...]

By | 2016-11-08T09:30:15+00:00 December 8, 2014|Categories: Bioinformatics, Biology, Statistics|Tags: |0 Comments

Venn diagrams: a visualization nightmare!

I was recently reading a paper (a very inspiring read mapper for RNA-Seq!).  At some point the authors wanted to present the overlap between splice junctions detected by 4 RNA-Seq read mappers and choose to do so using the ubiquitous Venn diagram (see Fig. 1).  I spent a few minutes staring at this colorful mosaic...  without gaining much insight. Fig. 1:  Example of a four-way Venn diagram. Reproduced from figure 4b of Genome Biology, 14(3):R30, 2013. Which mappers overlapped most in [...]

By | 2016-11-08T09:30:16+00:00 October 20, 2014|Categories: Bioinformatics, Data Visualisation, Statistics|0 Comments