Statistics – Page 3 – IRIC's Bioinformatics Platform

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 [...]

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 [...]