A: Data properties, preprocessing, p-value
16 important questions on A: Data properties, preprocessing, p-value
After normalization, we are left with random/measurement error in the data. It is important to know about the measurement error. How to proceed?
What is a random variable?
- A variable X whose value is determined by random processes
- Eg: counts
- Can be discrete or continuous
- real numbers, positive negatives
What is the event space?
- Higher grades + faster learning
- Never study anything twice
- 100% sure, 100% understanding
For my 1st exam I got a C. Then, I started looking for ways to learn better and I came across Study Smart. Since then I have scored a A+, A, A- and another A. I highly recommend it to everyone who wants to hear it. I am so happy with it!!
I was struggling to finish all my first-year subjects for 3 years. Then I discovered Study Smart, which helped me to finish all of them within 3 months.
Because of StudySmart, things are going well in many ways. Before, I always had study stress and no time for anything. Now I feel calm and confident (because of the program). I used to score a B, now I usually score an A or A+.
Hey Chris, I really want to thank you very much for developing the platform, I usually got around C for my exams, now I scored an A+, an A and a A- !!
Since using Study Smart, my average has increased significantly. I even completed a statistics course with a A+ while I'm bad at statistics. I took on extra courses this year, because of Study Smart. Thanks so much!
Ever since I started studying with StudySmart I passed all my exams !!! No more re-sits!! At first, I was happy with a pass and now I only get good grades. Many thanks!
I aced all the courses I studied with Study Smart. For law, I first scored a D, and now an A! I’m 100% sure that I’ll pass all the courses I study with Study Smart.
I always thought I studied well. My grades were fine. I could never have imagined that applying these study skills would have such a huge and direct impact on my grades, my speed and the pleasure I have in learning.
For the first time, I finally feel totally confident about the way I learn. I have the perfect overview and make great progress in terms of speed and the grades I get. Thanks, Chris!
I immediately started to enjoy learning again, and my grades soared. All of a sudden, everything went better. I highly recommend Study Smart to all students..
Being able to create my materials online made the process of studying so much smoother and quicker. I no longer have to spend a huge amount of my time on creating my summaries.
At first, my notes were a mess. Now I use Study Smart to take my notes in a perfectly structured way. It helps me to save a lot of time and do other things I enjoy.
Students that study with Study Smart get better grades. The system applies all the learning methods in such a way that both well-performing students and students who struggle perform much better.
Hi Chris, I would like to thank you very much. Last year I scored C on a course, and this year I got an A+ thanks to your method! Thank you very much!
The largest effect is that my child is more enthusiastic about school! Every parent wants their children to be happy at school, Study Smart made it happen.
In high school, I failed several exams, and that has really changed now. I actually needed this tool very much back then. Since I started studying with StudySmart, I haven't had any D's. My average score is now an A and those are results I would have never had in the past
With my old method, I passed only 3 out of 8 courses. Since I started taking my notes digitally in Study Smart, I have passed all my courses on the first try. For me, StudySmart takes away the stress of wondering if I will pass or not.
Thanks to StudySmart, I passed all my exams, and with better grades than before! On top of that, I have mastered a very good study method now, which I am confident will help me earn my degree.
What is a distribution function?
- binomial
- poisson
- normal
What is a null hypothesis?
When do we call variation in expression significant?
- More than 2-fold difference
- Top 20 of differences in expression
Objective criteria:
- 2-sample t-test
- With H0: mu1 = mu2 (so no difference)
What is proportional error?
--> heteroscedastic, so don't use a t-test.
But you can transform the value: take log of concentration
What is variance stabilisation?
- Transform the data in such a way that the variance becomes independent of the mean
- log transform when error is proportional to mean
- square root transformation for Poisson-distributed (count) data
- Transformed data are homoscedastic
- But may not have normal-distributed error! Should be investigated
- If this assumption is also met, you can apply t-test, ANOVA etc
What is lamba in the poisson distribution?
What is the simplest assumption you can make when looking at a number of counts?
What is an important characteristic of the poisson distribution?
We can use it to find out if a variable is poisson distributed.
How is the Poisson distribution applied to RNA seq?
- We can't use it directly: we don't have counts anymore but fractions
- But mean, variance relation still conserved, so use that!
- See slide
How would you proceed (RNAseq) with Poisson testing?
use poisson test --> p value
In a RNA-seq experiment, the reads per gene are not poisson distributed. What do we observe?
Check slide 39
How do we solve the problem of overdispersion?
- Sophisticated: Model the random error by Negative Binomial (NB) distribution and use suitable test statistic
- NB distribution = for discrete variables, and has two parameters instead of one
- In NB, sigma is independent of mu
- Poisson distribution is special case of NB
- Simple: Perform a variance stabilisation, approximate the random error by a Normal distribution and use a t-test
- pretends that we have a continuous variable
- Can be performed in a spreadsheet
- Uses common test statistic
Multiplex technologies lead to multiple hypotheses. Explain.
One for each gene!
Expression of gene X is equal under conditions A and B.
The question on the page originate from the summary of the following study material:
- A unique study and practice tool
- Never study anything twice again
- Get the grades you hope for
- 100% sure, 100% understanding
