The Baserate Fallacy, revisited

In which I share some iPython code for an interactive demo to calculate and visualise the probability that a positive test implies a positive result. You can get it here, and preview it here. Then I get entangled in a topic outwith my expertise.

ANI are you okay? Are you okay ANI?

In which I describe Average Nucleotide Identity (ANI), which we can use to pigeonhole bacteria into conceptual boxes labelled as 'species'. And I share more code.

A Nice New Paradox Redux: Paredux

In which I admit to a mistake.

A Nice New Paradox

In which I work through a popular statistical puzzle/paradox (with potential implications for interpretation of large data studies). With example code.

On Reciprocal Best BLAST Hits

In which I narrowly avoid a rant. Reciprocal best BLAST hits can improve the quality of your searching, and are a good way to find candidate orthologues. There's evidence and everything.

Dead fish, and multiple-test correction

In which a salmon is resurrected, but not enough to really be significant.  Why finding 20 positive results when your P-value threshold suggests you should only see 10 isn't necessarily anything to be excited about.  And an introduction to Bonferroni and Benjamini-Hochberg multiple test correction.

The Base Rate Fallacy in Effector-Finding

In which an oft-overlooked bit of genome-mining statistics is considered, and your enjoyment of a holiday could depend heavily on other people's hygiene.

New plots for old kinetics

In which basic enzyme kinetics are revisited, systematically incorrect lab statistics are bemoaned, and a little-known elegant 40 year old solution to estimating enzyme kinetic parameters is explored.