From 5ed1a0c1cf03c760522ef2ae0fcaaa5132e5d65d Mon Sep 17 00:00:00 2001 From: Emma Rand Date: Sun, 15 Oct 2023 10:17:42 +0100 Subject: [PATCH] add omics 2 overview to omics overivew page --- omics/omics.qmd | 27 +++++---------------------- 1 file changed, 5 insertions(+), 22 deletions(-) diff --git a/omics/omics.qmd b/omics/omics.qmd index 64c39c9..d4dc690 100644 --- a/omics/omics.qmd +++ b/omics/omics.qmd @@ -15,31 +15,14 @@ In the workshop, you will learn what steps to take to get a good understanding o ## Omics 2: Statistical Analysis -before - -- which genes matter: expression, DE -- goal of DE -- how does DE work -- multiple testing: FDR -- say what comparisons we will do - -workshop -- open project import the data -- revise! -- prep for DE -- lists of genes -- writing to files - -after - -- document what you have done -- repeat on another comparison +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`** [@DESeq2] or on logged normalised expression values using **`scran`** [@scran] or both. ## Omics 3: Visualising and Interpreting before - recap what we have +- PCA - volcano plot described - GO terms - @@ -47,13 +30,13 @@ before workshop -- open project import the data -- revise! +- PCA - volcano plot -- kable table? knitr::kable(df) |> kableExtra::kable_styling() - annotating with go terms after - document what you have done - repeat on another comparison + +References \ No newline at end of file