We're a little crazy, about science!

Archive for March, 2021

Caution: under pressure

For a third week in a row I’ve been instructed by my main-PI to give our lab virtual presentations on the work I’ve been doing. It’s been a point of stress now for almost a full month and doesn’t seem to be letting up any time soon. After every meeting I get a list of things I need to do before the following meeting and this time was no different, so today I guess we’re going to take a look at what exactly is next on my to-do list.

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On failure

Maybe it’s the hangover from yesterday’s news about my fellowship, but I feel like I got backed over repeatedly by a truck. Maybe it’s the uncertainty of the future, or all the work I still need to get done for tomorrow, maybe it’s a lot of things. Somedays I wish I could just pause, but I don’t think I’ve ever been able to stop and don’t really know what I would do with myself if I did. Actually I do know, since I can recall at least one time in my life where I hit the pause button and it didn’t end well.

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NDSEG fellowship result

Applying for a fellowship is sort of like creating a time capsule. The lag between when you submit it and when you hear anything back can be 6 or more months, long enough that you’ve completely forgotten that you applied. Or at the very least it isn’t at the forefront of your brain anymore. I’ve kept an eye on my application sporadically, I know people who check weekly and I’m sure there are plenty who don’t check at all until the results are sent out. It’s a slow motion car crash, you hope for the best, but it’s no longer in your control.

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The long data processing road

Okay I’m taking another break from the “in statistics” posts, at least for today since the next topic is going to be a long multi-day post worth of stuff and I need an easier post for today. I have way too much stuff going on at the moment to organize a long post! In any case, I figure I could give an update to the data I’ve been working with and how that whole mess is going. It’s mind numbing and exhausting work, but not in the way you would think.

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The Bonferroni correction in statistics

Well we’re doing it, today we’re talking about the Bonferroni correction, which is just one of many different ways to correct your analysis when you’re doing multiple comparisons. There are a lot of reasons you may want to do multiple comparisons and your privacy is our main concern so we won’t ask why. Instead we’re going to talk about how to adjust your alpha (chances of making a type 1 error) so you don’t end up making a mistake.

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One-tailed vs. two-tailed tests in statistics

Sit right back because we’re telling a troubling tale of tails full of trials, twists, and turns. The real question is, will we run out of words that start with t during this post? It will be tricky, but only time will tell. When do we use a two-tailed test vs. a one-tailed test and what do tails have to do with tests anyway? With a little thought, I think we can tackle the thorny topic. In short, let’s talk tails!

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The p-value in statistics

We’ve been dancing around the p-value for some time and gave it a good definition early on. The p-value is simply the probability that you’ve made a type one error, the lower the p-value the less chance you have of making a type one error, but you increase your probability that you’ll make a type two error (errors in statistics for more). However, just like with the mean, there’s more than meets the eye when it comes to the p-value so let’s go!

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The z-score in statistics

Okay, time to get back to statistics, if only for today! P-value, z-score, f-statistic, there are a lot of ways to get information about the sample of data you have. Of course, they all tell you something slightly different about the data and that information is useful when you know what the heck it is even trying to tell you. For that reason we’re diving into the z-score, it’s actually one of the more intuitive (to me anyway) measurements so let’s talk about it!

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Freedom of speech

I didn’t expect to have to talk this out, but here we are. Freedom of speech applies to the government, not private entities such as (but not limited to) twitter, facebook, schools, work, and basically any private place you congregate. Freedom of speech also does not mean freedom from consequences of that speech, you can’t talk about blowing up a school for example without consequences, even if it was a “joke.” More importantly, the government already ruled that certain hate speech isn’t protected. Why is this important? Well it’s a good reminder for the internet in general, but this time it’s a little closer to home reminder, namely the lab I work in.

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VA healthcare in a pandemic

With the pandemic stretching now over a year, which really feels like twenty, eventually healthcare was going to be an issue for me. I’ve already had to have a surgery during the pandemic, which was nerve wracking not because of the surgery, but because of COVID. Well it’s become a struggle to keep trying to put off getting care when I’m someone who needs pretty regular care. I went from bi-weekly appointments to once every 6 months or more, not ideal.

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EEG cleaning progress

Yesterday’s coding work went better than expected! That may or may not bode will for the rest of the week, but hey at least I’m sort of ahead of schedule. Today I figure we can take a quick look at what I’ve been doing with the data and why. This will be part informative and part me complaining about how everything has to be so damned hard (basically the usual around here). Mostly it will just be some visuals of the things I’ve had to change to get everything looking like my main-PI wants, he’s got a particular style he likes so a lot of large text, bolded labels, etc.

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The juggling act

The middle colorful plot, it’s called a spectrogram and if you notice the colorbar to the right has values ranging up to 25,000, that’s not right…

Blogging and coding and writing, oh my! There’s a lot to get done, seems like a running theme around here doesn’t it? If it were possible to clear some of it off my plate it wouldn’t be so bad, but the sad truth is deadlines seem to like to group together and there are quite a few coming up. Most of them are for my class so I can’t really miss those even if I wanted to. My research deadlines I can’t really miss either, not without some consequences anyway. So we’re back to juggling everything, but as we’ve seen in the past, I’m pretty good at this.

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The new to-do list

It’s been busy! So busy I was trying to find time to write while working on the million other things I have going on. Since I have a moment, I thought now would be as good a time as any to go over the big list my main-PI gave me to do before next week. It’s a long, long, long list and as you may expect, he’s pretty far removed from the situation, so I don’t think he realizes how difficult it is to do what he’s asking, but we’re doing any anyway! Thankfully I’ve gotten pretty good at coding, the bad side is that it’s not my code I’m working with, so that’s the start of my struggles.

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Twice the work, half the… fun?

I work with… Braiiiiins!! Well yesterday I touched on an experiment I did waaaay back in October-ish of last year! With the way things are going it feels like five years not 5 months, but what can you do? My main-PI has started to not so gently or subtly push me to process the data to his satisfaction and start working on the publication of the results. There’s been a lot going on that has pulled me away from the project, from the end of December to the middle of February I was working on grants, but now there isn’t a whole lot stopping me from working on this project almost exclusively… if you don’t include the other grant I’m writing and the fellowship I’m supposed to apply for.

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A PhD proposal defense

Not mine, at least not yet. A colleague of mine is defending his PhD proposal today and while I was going to wait until I did mine to go over the details about how that works and why we do it, I figured today was as good a time as any to do it. Besides I probably (definitely) repeat myself a lot around here, but that’s the catch with blogging daily. So let’s get into what a proposal defense is and why it’s important, shall we?

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COVID variants and our future

Awhile back I wrote a post on everything you needed to know about the COVID vaccine (here), I talked about the science, my experience with it (as someone who got vaccinated very early on), and more importantly why you should feel safe getting your shots too. Very ominously I mentioned that the target for the vaccine was the spike protein because it would (ideally, but not for sure) be conserved across mutations, well it’s time for an update and the news isn’t great.

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The mean in statistics

Yeah it seems simple, I mean (no pun intended) the mean is just the average! Yet as with so many different things in statistics there’s more to the mean than meets the eye! We’re going to go into why the mean is important, why it’s our best guess, why it may not always be your best option, and why we work so hard to find the mean sometimes! It seems simple, but I promise today we’re answering a lot of the big “why’s” in statistics, so let’s go!

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The Tukey test in statistics

No, not turkey, Tukey, although they are pronounced very similar (depending on who you ask I guess? I’ve seen people pronounce it “two-key”). Any way, today we’re saving our job and the wrath that comes with failure. The mad scientist boss of ours tasked us with testing mind control devices and determining statistically which one (if any) worked. After the last failure, we now had four new devices to test, so we couldn’t use the same method as before. However, an assistant’s work is never done, we didn’t finish the job! That’s what we’re going to do today.

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The ANOVA in statistics

Image from: Listening a great sci-fi movie (in my opinion)

Our mad scientist is back and this time they are not taking any chances! After statistical failure in the last example, they created not just one, but four mind control prototypes! We’ve been tasked with determining if they are working or face certain DOOOOOOOM! Sure, working for a mad scientist can be stressful, but we can do this… right? I’ve been dreading this post and you’ll see why, there’s a lot to cover before we solve the mystery, so let’s dive into it!

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Significance in statistics

That feeling when your p-value is lower than your alpha, aww yeah! But what does it really mean? It’s one thing to say there is significance and on the surface it means the two things are different “enough” to be considered two things, but I think there’s a simpler way to explain it. So today we’re going to talk about what significance actually means in the practical sense. Maybe it’s super obvious, but it never hurts to state it anyway.

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The f-test in statistics

Yep, we’re getting right back into it. I’m still working out things from yesterday, so we can just talk more statistics. This will be an interesting one and hopefully it will be pretty straightforward. The f-test, which in this case is really the f-test to compare two variances. You may have guessed, but the t-test uses the t-distribution (sort of like the normal), well the f-test uses the f-distribution, which is nothing like the normal! Let’s dive in, shall we?

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A roadblock

I haven’t spoken with my Co-PI about this yet because I’m angry. Like fist balled, white knuckled, want to scream into some endless void angry. This was not the post for today, but I’ve learned a long time ago that I should get things out instead of bottling it up and letting it eat me alive. It’s the reason I’m still here today and one minor step to my success in not falling into the abyss that is depression. I am angry and I need to chose my next words carefully, because as you’ll see, I have no power here.

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A meeting with my two PI’s

Yeah it feels pretty dangerous…

If I could make a comedy TV show about my life, I would call it my two PI’s and I would get into hilarious situations while trying to make both of them happy. Mostly you would see me get a lack of sleep and sort of feel like I’m running on a treadmill, going as fast as I can, but getting nowhere. It’s not all bad and I respect my two PI’s, but there’s a saying about having too many hands in the cookie jar and sometimes it feels like that’s what is happening. It’s a lot like the old game “telephone” where I’m given information to pass along between the two, so we’re all going to meet… *cue dramatic music*

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First project deadline!

I didn’t have anything particularly lined up for today to add to the “in statistics” posts I’ve been doing, so today I thought it may be better to outline what I’m doing in the statistics course I’m taking. At the very least it may help me get it done, because as usual around here, the project is due… today. Yep, it’s yet another mad dash to the finish. Will I make it? Will I ever figure out what statistics is? Will I learn to stop asking questions in this format? Find out all this and more!

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Confidence intervals in statistics

Wait… this is the wrong kind of confidence!

Well since our mad scientist from yesterday’s post is on a short break, today we’re going to fill in some of the gaps that post brought into view. First up is the confidence interval. There are some subtle points here, so this should help clarify a few things that may not have been clear yesterday. We’re going to do a somewhat deep dive into what the heck we’re doing when we talk confidence interval and why the standard deviation of our data is important in determining the values.

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The t-test in statistics

mind reading

Welcome fellow mad scientist enthusiasts, the last time we talked statistics, we found ourselves in an interesting situation and we need to figure out if the mind control device that was developed is actually working. We introduced the idea of a two population problem and today we’re going to use something called a t-test to determine if our mad scientist succeeded.

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We interrupt your regularly scheduled programing…

This is not the post you are looking for. Error, please try again. Okay, seriously I need to get some work done today and I don’t have time to solve our mysterious mind control device problem that I posed yesterday, so today I’m going to give some quick thoughts on something totally unrelated because there isn’t time for anything else and while trying to figure out a header for this post (where I was originally going to say hey can’t talk today) I was reminded of max headroom. I genuinely don’t know that I’ve ever said that before, but here we are…

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Two populations in statistics

As a mad scientist, or maybe just a grumpy scientist, you want to test a new mind control technique! To do this you decide that you want to test this works by having people select one of two objects set in front of them. *Insert evil laugh* Using your mind control technique you want your unwitting participants pick the object on the left. You don’t get 100% success, but suspect it’s working, how do we know for sure?

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A fair coin in statistics

It has been a busy day, but the show must go on so to speak and I’m here today to tell you I have a nice shiny new coin for us to flip! The catch you may ask? Well it could be a fair coin or I may have just swapped it out for a coin that was not fair! Our goal is to see if I’m being sneaky and to do that we’re going to need some statistics!

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The central limit theorem in statistics

Today we’re gonna push it to the limit! The central limit theorem that is. It’s a cornerstone in statistics and the short and dry version is that it lets us turn any distribution we have into a normal distribution. If it wasn’t for the central limit theorem statistics would hurt far worse than it does now (speaking as someone taking a stats class now). For the longer version we need to discuss why a normal distribution is needed, why we prefer to work with them!

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Effect size in statistics

Imagine our population data is the red curve and our sample data is the blue and the post will help you make sense of it.

We’ve been talking statistics for the past few days and today we’re talking effect size. The short explanation is effect size is the difference between two conditions! The bigger the effect size, the easier it is to tell the two conditions apart, easy… right? There’s a lot that goes into determining effect size, after all it’s hard to know what your effect size is without having some prior knowledge about what you’re groups look like, so let’s go into some detail.

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