Matthew Young's Blog - Mostly maths, programming and science.

Estimating the copy number rate per cell division

Uniparental disomy constrains the rate of mitotic nondisjunction

Posted on April 4, 2022

I recently happened across this paper, which I found quite astonishing. Firstly, it’s written by the 23andMe research team. If there’s still anyone in need of convincing that important and exciting research happens in industry, they should read this paper, because it is high quality and the data they have... [Read More]

Linear Regression

Developing intuition for regression coefficients

Posted on December 24, 2020

Linear regression is one of those things that is easy to use in practice, but difficult to develop a good intuition for. At least I struggle to have a good sense of what the regression coefficients are going to look like for all but the most trivial cases. [Read More]

Reproducible analysis for the very lazy

Posted on December 6, 2020

These days, pretty much everyone acknowledges that scientific analysis should be reproducible. Of course, this is still very often not the case. For the most part, I don’t think that people start out trying to write code and structure their data so no one else can reproduce their results. But... [Read More]

Batch effects in single cell RNA sequencing

Part 2 - Handling batch effects without batch correction

Posted on October 24, 2020

In a previous post, I wrote about the perils of over-diagnosing batch effect. In this post I’m going to do something even more controversial and provide advice for how to deal with batch effects without using some black box “batch correction” tool. Why would you want to do this? Are... [Read More]

Batch effects in single cell RNA sequencing

Part 1 - Diagnosing batch effects from UMAP

Posted on June 9, 2020

With the ever increasing number of single cell transcriptomics data sets available, people are wanting to do combined analyses more and more frequently. Of course, the first thing that happens when people do this is that data from different samples, labs, and experiments don’t “mix well”. The identification of poor... [Read More]