From 7878b048cd777e2bf89447c89da572f628fd4ed8 Mon Sep 17 00:00:00 2001 From: Ashley Sawle Date: Mon, 30 Sep 2024 13:24:12 +0100 Subject: [PATCH] Slight change to final exercise --- Markdowns/08_DE_analysis_with_DESeq2.Rmd | 7 +- Markdowns/08_DE_analysis_with_DESeq2.html | 171 +++++++++++++++------- Markdowns/08_DE_analysis_with_DESeq2.pdf | Bin 6003154 -> 6003344 bytes 3 files changed, 119 insertions(+), 59 deletions(-) diff --git a/Markdowns/08_DE_analysis_with_DESeq2.Rmd b/Markdowns/08_DE_analysis_with_DESeq2.Rmd index 16a9883..2280c97 100644 --- a/Markdowns/08_DE_analysis_with_DESeq2.Rmd +++ b/Markdowns/08_DE_analysis_with_DESeq2.Rmd @@ -7,6 +7,7 @@ output: toc: yes html_document: toc: yes + toc_float: true bibliography: ref.bib --- @@ -531,11 +532,11 @@ gene expression between days 11 and 33. > > Let's investigate the uninfected mice > -> 1. Extract the results for d33 v d11 for Uninfected mice. +> 1. Extract the results for d33 v d11 for Infected mice. > How many genes have an adjusted p-value less than 0.05? -> Is this remarkable? -> 2. Extract the results for d33 v d11 for Infected mice. +> 2. Extract the results for d33 v d11 for Uninfected mice. > How many genes have an adjusted p-value less than 0.05? +> Is this remarkable? > > Do these results suggest another approach to analysing this data set? diff --git a/Markdowns/08_DE_analysis_with_DESeq2.html b/Markdowns/08_DE_analysis_with_DESeq2.html index 6d9d941..8442c0c 100644 --- a/Markdowns/08_DE_analysis_with_DESeq2.html +++ b/Markdowns/08_DE_analysis_with_DESeq2.html @@ -29,6 +29,9 @@ h6 {font-size: 12px;} code {color: inherit; background-color: rgba(0, 0, 0, 0.04);} pre:not([class]) { background-color: white } + + + @@ -176,6 +179,69 @@ + + + @@ -185,6 +251,16 @@
+ +
+
+
+
+
+ +
+ + -

1. R packages for differential gene expression analysis

@@ -464,9 +492,9 @@

Exercise 2

  • how many genes are significantly (with an FDR < 0.05) down-regulated?

  • Here is the results table for two of the genes:

    • -
    - -

    One of these is strongly downregulated with log2(fold-change) of \(-2.46\). On a linear scale this is \(2^{2.46} = 5.5\) times more highly expressed in the unifected group relative to the infected group. However its adjusted p-value is \(0.27\). By contrast, the other gene has a lower LFC ~ \(-1.61\) (on a linear scale \(2^{1.61} = 3.05\)) but it’s adjusted p-value is 0.0023.

    +
    + +

    One of these is strongly downregulated with log2(fold-change) of \(-2.46\). On a linear scale this is \(2^{2.46} = 5.5\) times more highly expressed in the uninfected group relative to the infected group, but its adjusted p-value is \(0.27\). By contrast, the other gene has a lower LFC ~ \(-1.61\) (on a linear scale \(2^{1.61} = 3.05\)), but it’s adjusted p-value is 0.0023.

    How can you explain this apparent contradiction?

    @@ -620,12 +648,12 @@

    Exercise 7

    Let’s investigate the uninfected mice

      -
    1. Extract the results for d33 v d11 for Uninfected mice.
      +
    2. Extract the results for d33 v d11 for Infected mice.
      How many genes have an adjusted p-value less than 0.05?
      -Is this remarkable?
      3. -
    3. Extract the results for d33 v d11 for Infected mice.
      -How many genes have an adjusted p-value less than 0.05?
      4. +
    4. Extract the results for d33 v d11 for Uninfected mice.
      +How many genes have an adjusted p-value less than 0.05?
      +Is this remarkable?

    Do these results suggest another approach to analysing this data set?

    @@ -657,6 +685,8 @@

    10. Save the results

    +
    +
    @@ -689,6 +719,35 @@

    10. Save the results

    +