Assessing enrichment

Working on a set of RNA-seq of AML patient samples, I stumble on gene X.  When its expression is high, 50% of the samples are mutated on gene Y, a mutation that has a prevalence of only 20% in the rest of the dataset.  Is there a link between these two observations?  Let's put some numbers on this:  among the 131 samples of the dataset, 28 show mutations on gene Y, 6 have high expression of X and 3 have both "features".  The table below is [...]

By | 2017-04-29T15:49:00+00:00 May 21, 2014|Categories: Bioinformatics, Statistics|0 Comments

lifelines (or doing survival analysis in Python)

Lately, I've been doing survival analysis.  I'm not an expert but we had a self-learning group based on David G. Kleinbaum and Mitchel Klein’s  book,   "Survival Analysis. A Self-Learning Text" .  At the end of this book, there's code provided to help you get started in SAS, Stata, SPSS and... R!  I've played with the R package survival which is quite good!  My problem was that I wanted to do survival analysis in Python.  I've started by doing it with [...]

By | 2017-04-29T17:16:41+00:00 March 24, 2014|Categories: Data Analysis, Python, Statistics|Tags: |0 Comments