Data Analysis

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 | 2017-04-29T17:47:57+00:00 January 13, 2017|Categories: Data Analysis|Tags: , , |0 Comments

Pivoting tables : from long to wide

As bioinformaticians, we often have to work with data that are not formatted the way we would need them to be. One case we might encounter is receiving data in a "long" format instead of receiving them in a more familiar "wide" format. For those of you familiar with the ggplot R package, you know this format very well. It's the format required by ggplot to produce its nice graphs.   Long genes samples expression 1 BAD S01 7.525395 2 [...]

By | 2017-04-29T18:11:56+00:00 November 14, 2016|Categories: Data Analysis, Python, R|Tags: |0 Comments

Bootstraps and Confidence Intervals

When analyzing data, you might want or need to fit a specific curve to a particular dataset. This type of analysis can result in instructive outputs regarding the relationship between two (or more...) quantifiable parameters. The main object of this post is not how to implement such fitting, but rather how to display the goodness of such a fit i.e. how to calculate a confidence interval around a fitted curve. That being said, I will show how to do curve fitting in [...]

By | 2017-04-29T18:33:55+00:00 September 29, 2016|Categories: Data Analysis, R, Statistics|Tags: |1 Comment

SciPy and Logistic Regressions

Given a set of data points, we often want to see if there exists a satisfying relationship between them. Linear regressions can easily be visualized with Seaborn, a Python library that is meant for exploration and visualization rather than statistical analysis. As for logistic regressions, SciPy is a good tool when one does not have his or her own analysis script. Let's look at the optimize package                        from scipy.optimize import [...]

By | 2017-04-29T16:58:35+00:00 June 9, 2016|Categories: Data Analysis, Python|Tags: , |0 Comments

What to consider when interpreting proteomic data

** Special collaboration from the proteomic platform** Following your sample's analysis by mass spectrometry, you will usually receive your results as a list of proteins.    During the treatment of the data, some factors inevitably influence the proteins found in the final list. Fig. 1 Overview of bottom-up proteomics. Figure modified from Angel et al. (2011)   Let's begin by briefly explaining how this protein list is generated by the bottom-up approach usually used (see Figure 1).  In this [...]

By | 2017-04-29T17:08:11+00:00 December 7, 2015|Categories: Data Analysis|Tags: |0 Comments