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--- | ||
title: "Visualisation of Differential Expression Results" | ||
date: "October 2024" | ||
output: | ||
ioslides_presentation: | ||
css: css/stylesheet.css | ||
logo: images/CRUK_Cambridge_Institute.png | ||
smaller: yes | ||
widescreen: yes | ||
beamer_presentation: default | ||
slidy_presentation: default | ||
--- | ||
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## Differential Gene Expression Analysis Workflow {#less_space_after_title} | ||
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<div style="line-height: 50%;"><br></div> | ||
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<img src="images/01s_workflow_3Day.svg" class="centerimg" style="width: 80%; margin-top: 60px;"> | ||
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## Spoiler Alert: Plots we are going to make | ||
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<img src="images/10s_plotSpoilers.svg" class="centerimg" style="width: 90%; margin-top: 60px;"> | ||
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## Shrinkage | ||
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When counts are low the variance is high | ||
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Eg. | ||
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* sample 1 = 2, sample 2 = 4 (large variance) | ||
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* sample 1 = 90, sample 2 = 100 (small variance) | ||
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Makes those genes appear more significant than they really are on plots | ||
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So we need to `shrink` the logFCs. | ||
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<img src="images/10s_MAplots.png" class="centerimg" style="width: 60%; margin-top: 10px;"> | ||
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## ggplot2 library | ||
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* Basic syntax for building a plot | ||
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<div style="width: 45%; | ||
float: left;"> | ||
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<div style="padding-top: 20px; | ||
padding-bottom: 20px;"> | ||
<img src="images/10s_ggplot_1.png" class="centerimg" style="width: 95%"> | ||
</div> | ||
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</div> | ||
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<div style="width: 45%; | ||
float: right;"> | ||
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<div style="padding-top: 20px; | ||
padding-bottom: 20px;"> | ||
<img src="images/10s_ggplot_2.png" class="centerimg" style="width: 95%"> | ||
</div> | ||
<div> | ||
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