Blog of Andrés Aravena
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# Methodology of Scientific Research

## How Science Works

08 March 2021

This course focus in theoretical and practical aspects of doing science. In particular we learn how to design good experiments that can create high-impact knowledge. This year we will focus on gene expression experiments.

This will be a very practical course, in the understanding that there is nothing more practical than a good theory.

# Classes

Here you will find the slides from the classes and other supplementary material. Notice that some things are said but not written, so you better take good notes. We recommend taking notes with pen and paper using the Cornell Method.

• Class 1: Why? How?. (Mar 17, 2021). [Video],[Video],[Slides].
What is the scientific method? Why do we care? How can we do better science?
• Class 2: Statistical significance. (Mar 24, 2021). [Video],[Slides].
Finding which genes (probably) change their expression.
• Class 3: Introduction to Probabilities. (Mar 31, 2021). [Video],[Slides].
What do we mean by “genes that probably change their expression”?
• Class 3.1: Why everybody should learn math . (Mar 31, 2021). [Slides].
What do we mean by “genes that probably change their expression”?
• Class 4: Probabilities. (Apr 7, 2021). [Slides].
Decomposing complex events into simple ones where it is easy to calculate probabilities.
• Class 4.1: Diagnostics and classification. (Apr 7, 2021). [Slides].
Why a 99% diagnostic is not what you think
• Class 4.2: Bayes Theorem. (Apr 7, 2021). [Video],[Slides].
How do we learn from experience
• Class 5: Random Variables. (Apr 14, 2021). [Slides].
Why a 99% diagnostic is not what you think
• Class 6: Chebyshev Inequality. (Apr 28, 2021). [Slides].
What can we say about the next experiment outcome?
• Class 6.1: Law of Large Numbers. (Apr 28, 2021). [Slides].
How can we know the population mean?
• Class 6.2: Estimating the population variance . (Apr 28, 2021). [Slides].
How can we guess the population variance?
• Class 7: Central Limit Theorem. (May 5, 2021). [Slides].
What happens when 𝑛 is large? Can we have narrower intervals? Can we know better?
• Class 7.0: Why do we need theory?. (May 5, 2021). [Slides].
Shall we focus on “how to calculate”? It is better to learn why we calculate and when not to do so.
• Class 8: What is a 𝑝-value?. (Jun 2, 2021). [Slides].
Humans are good at finding patterns. Too good sometimes. This is one way to see if the pattern is real or not.
• Class 9: Linear Models & Enrichment. (Jun 9, 2021). [Slides].
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# Plan

• How to measure gene expression
• qPCR, microarrays, RNAseq
• How to find gene expression data online
• NCBI, EBI, others
• How to analyze gene expression results
• parametric tests
• contrasts
• How to normalize gene expression data
• qPCR
• microarray
• RNAseq
• How to design a good experiment: Analyze before doing the experiment
• See what are the important variables
• See what are the error sources