Merge pull request #13 from 3mmaRand/fix

add omics 2 overview to omics overivew page

omics/omics.qmd

@@ -15,45 +15,28 @@ 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
 -   
 
 
 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