From dedfa9f7d4972bdd9d35d3a82964612ad9f12d9d Mon Sep 17 00:00:00 2001
From: hpolvech <helene.polveche@ens-lyon.fr>
Date: Thu, 14 Oct 2021 10:17:11 +0200
Subject: [PATCH] Thresholds
---
session_4/session_4.Rmd | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/session_4/session_4.Rmd b/session_4/session_4.Rmd
index 46b7df4..a5fa1ec 100644
--- a/session_4/session_4.Rmd
+++ b/session_4/session_4.Rmd
@@ -560,7 +560,20 @@ Open the csv file using the `read_csv2()` function. The file is located at "http
```{r read_csv2}
tab <- read_csv2("http://perso.ens-lyon.fr/laurent.modolo/R/session_4/EWang_Tibialis_DEGs_GRCH37-87_GSE86356.csv")
-expr_DM1
+tab
```
</p>
</details>
+
+To make a Volcano plot, displaying different information about the significativity of the variation thanks to the colors, we will have to make a series of modifications on this table.
+
+We will have to create :
+
+- a column 'sig' : it indicates if the gene is significant ( TRUE or FALSE ).
+**Thresholds :** baseMean > 20 and padj < 0.05 and abs(log2FoldChange) >= 1.5
+
+- a column 'UpDown' : it indicates if the gene is Up regulated or Down regulated.
+
+
+
+
--
GitLab