From 628dc2713926b339d683826c8afc991d0cd62432 Mon Sep 17 00:00:00 2001 From: January Weiner Date: Thu, 3 Oct 2024 17:53:07 +0200 Subject: [PATCH] updated presentation --- how-to-talk-to-your-bioinformatician.html | 267 ++++++---------- how-to-talk-to-your-bioinformatician.qmd | 360 +++++++++++++--------- images/pregnant.jpg | Bin 0 -> 28004 bytes 3 files changed, 315 insertions(+), 312 deletions(-) create mode 100644 images/pregnant.jpg diff --git a/how-to-talk-to-your-bioinformatician.html b/how-to-talk-to-your-bioinformatician.html index 81ba9b8..2834ee4 100644 --- a/how-to-talk-to-your-bioinformatician.html +++ b/how-to-talk-to-your-bioinformatician.html @@ -3134,64 +3134,22 @@

How to talk to your bioinformatician?

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Part I

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Who am I to tell you things?

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Slide 1

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Bioinformatics vs statistics vs computational biology

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Bioinformatics, statistics, computational biology

Things bioinformaticians care about

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  • Experimental design
  • The biological question
  • Statistics
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  • Experimental design
  • Reproducibility
  • File formats
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Experimental design

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How many samples are sufficient?

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  • Depends on the question
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  • Depends on the technology
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  • Depends on the variability
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How many samples are sufficient?

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The bottom line

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Talk to your bioinformatician early!

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Statistics

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Why is that important?

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Experimental design

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How many samples are sufficient?

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  • Depends on the question
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  • Depends on the technology
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  • Depends on the variability
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How many samples are sufficient?

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Say, we want to compare two groups with a standard \(t-test\), nothing fancy. Our ability to detect the differences (the statistical power) depends on the sample size and the effect size1.

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How many samples are sufficient?

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The \(y\) axis on this plot shows how the power of the test – meaning how often, assuming that the groups really differ by \(d\) on average, you will be able to detect the difference using a t-test.

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How many samples are sufficient?

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What about the following setup:

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  • We have 2 strains (WT and KO)
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  • We have treatment + control
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  • We want to know whether the treatment has a different effect on the KO strain than on the WT strain
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This is a 2x2 design, and we need to consider the interaction term.

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How many samples are sufficient?

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How many samples are sufficient?

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That is not even the worse thing.

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Simple calculations show that assuming

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  • your power is 80% (really great!)
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  • \(p-value\) cutoff is \(0.05\)
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  • 90% of the \(H_0\) are true (i.e., 10% of the time the differences are real)
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then 36% of your “significant” results are false positives1!

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(Plus, you failed to detect 20% of the real differences)

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The bottom line

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Talk to your bioinformatician early!

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How we work

  • Fine-tuning the analysis results
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    Identifiers

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    Excel and gene names

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    Excel and gene names

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    Excel and gene names

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    Don’t combine values and comments

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    How (not to) work with Excel

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    Thank you

    You can find this presentation along its source code at https://github.com/bihealth/howtotalk

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    Sources

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    • Source 2
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    Thank you

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    Slide 1

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    To compile, type quarto render template.qmd

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    Make sure you have Quarto 1.2 installed from here.

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    Multicolumn slide

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    Left column title

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    Left column…

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    Right column title

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    Right column (60%)…

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    (adding .fragment causes the contents to be displayed in steps)

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    Part II separator slide

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    Simple numbered and unnumbered lists

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    • Two
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    1. One
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    3. Two
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    Incremental list

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    • Item 1
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    • Item 2
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    • Item 3
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    Incremental contents

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    First part

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    Second part

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    This is a slide without a title (use the dashes to separate)

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    Transitions

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    Define them in the YAML header or like here, in the slide title.

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    Types: none, fade, slide, convex, concave, zoom

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    Code

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    plot(1:10)
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    -Figure 1: A dumb plot -
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    Tip

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    Ctrl-click on the image to zoom. And here is a 3.1415927 for you.

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    Code

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    There are many customization options for the code. For example, you can highlight (and even animate) certain lines of code:

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    a <- rnorm(10)
    -b <- rnorm(10) + a
    -c <- a + b * rnorm(10)
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    You can also specify where precisely should the output of the code go: below the code (default), on the next slide, on a right-hand column…