From 382496ba75b79b03949dccc3a5df1c48b98acb4f Mon Sep 17 00:00:00 2001 From: Emma Rand Date: Fri, 13 Oct 2023 14:00:49 +0100 Subject: [PATCH] overview with LO added; and hope a commit sorts the deploy issue :) --- omics/week-4/overview.qmd | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/omics/week-4/overview.qmd b/omics/week-4/overview.qmd index 6f08bcc..f109d10 100644 --- a/omics/week-4/overview.qmd +++ b/omics/week-4/overview.qmd @@ -5,8 +5,8 @@ toc: true toc-location: right --- -This week you will .... The independent study will ... -In the workshop, you will learn ... +This week we cover differential expression analysis on raw counts or log normalised values. The independent study will allow you to check you have what you should have following the [Omics 1: Hello Data workshop](../week-3/workshop.html) and [Consolidation study](../week-3/study_after_workshop.html). It will also summarise the concepts and methods we will use in the workshop. +In the workshop, you will learn how to perform differential expression analysis on raw counts using **`DESeq2`** or on logged normalised expression values using **`scran`** or both. We suggest you sit together with your group in the workshop. @@ -14,30 +14,31 @@ We suggest you sit together with your group in the workshop. The successful student will be able to: -- xxx -- xxx -- xxx -- xxx +- verify they have the required RStudio Project set up and the data and code files from the previous Workshop and Consolidation study +- explain the goal of differential expression analysis and the importance of normalisation +- explain why and how the nature of the input values determines the analysis package used +- describe the metadata needed to carry out differential expression analysis and the statistical models used by **`DESeq2`** and **`scran`** +- find genes that are unexpressed or expressed in a a single cell type or treatment group +- perform differential expression analysis on raw counts using **`DESeq2`** or on logged normalised expression values using **`scran`** or both. +- explain the output of differential expression: log fold change, p-value, adjusted p-value, ### Instructions 1. [Prepare](study_before_workshop.qmd) - i. 📖 Read xxx + i. 📖 Read what you should have so far and about concepts in differential expression analysis. 2. [Workshop](workshop.qmd) - i. 💻 xx + i. 💻 Find unexpressed genes and those expressed in a single cell type or treatment group. - ii. 💻 xx + ii. 💻 Set up the metadata for differential expression analysis. - iii. 💻 xx + iii. 💻 Perform differential expression analysis on raw counts using **`DESeq2`** or on logged normalised expression values using **`scran`** or both. - iv. 💻 xx - - v. 💻 Look after future you! + iv. Look after future you! 3. [Consolidate](study_after_workshop.qmd)