diff --git a/day01.html b/day01.html index 6990e2a..f57767d 100644 --- a/day01.html +++ b/day01.html @@ -398,7 +398,7 @@

DESeq2 Analysis with R: Part 01

Thomas Manke @ MPI-IE

-

Tue May 14 22:36:48 2024

+

Tue May 14 23:57:01 2024

diff --git a/day02.html b/day02.html index ddfb5cd..981d6ab 100644 --- a/day02.html +++ b/day02.html @@ -398,7 +398,7 @@

DESeq2 Analysis with R: Part 02

Bioinfo-Core @ MPI-IE

-

Tue May 14 22:37:00 2024

+

Tue May 14 23:57:13 2024

@@ -780,19 +780,18 @@

Normalization and size factors

sequencing depth and gene length -DESeq2 median of ratios +DESeq2 size factor sequencing depth and RNA composition

… and many others exist.

DESeq2 Workflow for the ‘median of ratios’:

- +
+ +
DESeq2 sizefactor determination.
+

Task (5 min): Plot a heatmap of the first 10 genes (rows) of the counts matrix and add the metadata after DESeq was run as @@ -1123,10 +1122,10 @@

Model fit and testing

dds_res %>% 
   data.frame() %>% 
   subset(padj < 0.05) %>% 
-  arrange(abs(log2FoldChange), descending=TRUE) %>% head(20)
+ arrange(-abs(log2FoldChange)) %>% head(20)
diff --git a/day03.html b/day03.html index 30aa6c0..f544ecd 100644 --- a/day03.html +++ b/day03.html @@ -398,7 +398,7 @@

DESeq2 Analysis with R: Part 03

Bioinfo-Core @ MPI-IE

-

Tue May 14 22:37:27 2024

+

Tue May 14 23:57:39 2024

diff --git a/day04.html b/day04.html index e209738..9583185 100644 --- a/day04.html +++ b/day04.html @@ -398,7 +398,7 @@

deseq2 - applied

Bioinfo-Core @ MPI-IE

-

Tue May 14 22:40:02 2024

+

Wed May 15 00:00:13 2024

diff --git a/images/DESeq2_sizefactor.jpeg b/images/DESeq2_sizefactor.jpeg new file mode 100644 index 0000000..ef59a3d Binary files /dev/null and b/images/DESeq2_sizefactor.jpeg differ diff --git a/images/Wald_LRT.jpeg b/images/Wald_LRT.jpeg index 1bc1763..beb4621 100644 Binary files a/images/Wald_LRT.jpeg and b/images/Wald_LRT.jpeg differ diff --git a/index.html b/index.html index cb19cbc..dc08234 100644 --- a/index.html +++ b/index.html @@ -398,7 +398,7 @@

DESeq2 Analysis with R: Description

Bioinfo-Core @ MPI-IE

-

Tue May 14 22:40:26 2024

+

Wed May 15 00:00:37 2024

diff --git a/outline.html b/outline.html index a956488..105bc01 100644 --- a/outline.html +++ b/outline.html @@ -398,7 +398,7 @@

DESeq2 Analysis with R: outline

Bioinfo-Core @ MPI-IE

-

Tue May 14 22:40:26 2024

+

Wed May 15 00:00:37 2024

diff --git a/summary.html b/summary.html index c51ebe4..09af397 100644 --- a/summary.html +++ b/summary.html @@ -398,7 +398,7 @@

DESeq2 Analysis with R: outline

Bioinfo-Core @ MPI-IE

-

Tue May 14 22:40:27 2024

+

Wed May 15 00:00:37 2024