Lab Statistics & Math

Now that we’ve learned about the role of apoptosis in good health and disease, it will be useful to know how we can detect apoptosis in cells or organisms. A variety of apoptosis detection kits are commercially available, and here is a roundup of how they work: TUNEL and DNA damage assays The TUNEL assay…

Your lab is full of non-chemical hazards that can explode, stab, kill, and – as if that wasn’t enough – bite.  Here’s a list of those hazards to remind you why Environmental Health & Safety exists! 1.  Centrifuges Centrifuges are dangerous, especially when not cared for!  An unmaintained ultracentrifuge imploded in an American lab in…

Let’s play a game. I’ll say a word and you say what comes to your mind. Ready? Go! Cat… Kitchen… Doctor… Airplane… Nobel… I have no idea what you said when I said cat but I’d say most of you said “prize” when I said Nobel. Alfred Nobel’s name is most often remembered because of…

The thing that was most difficult for me as an R beginner was plotting graphs with error bars – there is no concise way to do this with base graphics. There are workarounds, often using the ‘arrows’ command, but isn’t there a simpler way? Yes, in fact there are a handful of plotting packages for…

We’ve been slowly coaxing you along in our R tutorials.  We’ve introduced what R is, gave you a basic tutorial into how to use R and also spent some time learning how to explore your data with R. By now you are probably itching to use R for more complicated analyses.  To indulge you, I…

As you’ve probably kind of guessed from our previous articles Introducng R and the Basic R Tutorial, we think R programming language and R-studio are great tools for data analysis and figure production.  And now we are about to prove it! So, you’ve collected some data and are pretty sure you know what statistical test…

So you’ve performed a test such as an ANOVA and have found that there is statistical significance in your data (lucky you!), however you now want to know where that significance lies. When you are comparing multiple sets of data it might seem like a logical thought to simply perform an individual t-test between each…

Last week I focused on the left-hand side of this diagram and talked about statistical tests for comparing only two datasets.  Unfortunately, many experiments are more complicated and have three or more datasets.  Different statistical tests are used for comparing multiple data sets. Today I will focus on the right side of the diagram and…

The first hurdle in learning about statistics is the language.  It’s terrible to be reading about a particular statistical test and have to be looking up the meaning of every third word. The type of data you have, the number of measurements, the range of your data values and how your data cluster are all…

Scientific success is often defined by how well your experiments progress and the results you produce. However, scientific research is driven by a curiosity about the unknown, and you cannot always be prepared for the unknown. Inevitably there will come a time when your experiments fail. In this article I give you some of the…

The clock strikes 10:00 pm, your thumb has a raging case of carpal tunnel syndrome, the trash is full of tubes containing unsuccessful PCR reactions, and you wonder…Is this really what I want to do with my life? How do you get your mojo back when you’re knee deep in research?  One option to consider…

This guide is full of very simple but effective tips so you can have a pleasant lab experience, and help create a happy lab.

Math is an important part of lab life, from making solutions to calculating protein concentrations, and miscalculations can cause mayhem for your experiments. Therefore it is important that your math is right, or you could spend weeks trying to figure out what’s going wrong in your experiments. I was hopeless at remembering how to do…

In the previous article, I showed you how to interpret mean-squared displacement (MSD) and showed four easy things you can learn from an MSD graph at a quick glance. Now let’s turn from analyzing an MSD plot to making one. I am going to use the programming language R to generate simulated data and then…

So now you’re convinced that R is the language for you, you’ve downloaded R-Studio (from http://www.rstudio.com/) and opened it, and. . .what the hell do you do now? Great question! I always find it easiest to learn by doing something, rather than just by seeing a list of possibilities, so here I’ll walk you through…

Working with large datasets can be very frustrating and time consuming.  If only there were more tools out there to simplify things without needing to invest a PhD’s worth of time to learn how to use them! I am here to tell you that there is a solution, and a free one at that. If…

Like many scientists, I don’t consider myself a statistics expert. But I am determined to do things right in my science, and that includes statistics. In my experience, a lot of scientists who are “scared” of statistics fall into the trap of ignoring the existence of anything beyond a t-test. But using the right method…

To pull together our discussions so far on hypothesis testing and p-values, we will use the t distribution as an example to see how it all works. The t distribution (you may have heard it called Student’s t) is a probability distribution that looks like a bell-shaped curve (or normal distribution). If we sample repeatedly from…

Now we come to the third part of our trifecta; in the last two posts I have gone over p-values and how they determine significance in null hypothesis testing, and we talked about degrees of freedom and their effect on the p-value. Finally, we come to pseudoreplication: where it can all go terribly wrong. Replication…

In the last post I talked about p-values and how we define significance in null hypothesis testing. P-values are inherently linked to degrees of freedom; a lack of knowledge about degrees of freedom invariably leads to poor experimental design, mistaken statistical tests and awkward questions from peer reviewers or conference attendees. Even if you think…

In previous articles, I’ve primed you on hypothesis testing and how we are forced to choose between minimising either Type I or Type II errors. In the world of the null hypothesis fetish, the p-value (p) is the most revered number. It may also be the least understood. The p-value is the probability, assuming the…

This column is loaded with pop quizzes for you to test yourself on. If you haven’t already done so, catch up on yesterday’s piece on hypothesis testing for a refresher. Take a gander at the table below for a summary of the two types of error that can result from hypothesis testing. Type I Errors occur…

Hypothesis testing is the foundation around which we prove our science is worth funding, publishing and sitting through a conference presentation for. I can’t overstate the  importance of understanding hypothesis testing, such is the integral part it plays in biological analyses. The Null Hypothesis Fundamental to statistics is the concept of a null hypothesis, and…

In this, the first in a series of articles on statistics, I want to set out some of the main reasons why you, as a biologist, should improve your knowledge of statistics. The general consensus is that biologists are not strong when it comes to statistics. There’s nothing in our brains that stops us from…

Greg Petsko, President of the American Society for Biochemistry wrote a very interesting article recently in which he drew attention to the parallels between the PhD/Postdoc system and the medieval trade guilds, and the problems our profession faces because it is drifting away from that system. In the trade guild system the right of an…

….statistics. The very word strikes fear into the heart of many a biologist (including me). In an article published earlier this year, Cumming and co-workers of La Trobe University, Melbourne gave a very useful rundown of common mistakes made when using statistical error bars in biology and suggested a number of rules that should be…