From 733d5cc922c8c5503eb5d4c8528988d438872a95 Mon Sep 17 00:00:00 2001
From: Elizabeth Partan <36081569+epartan@users.noreply.github.com>
Date: Thu, 14 Nov 2024 11:28:00 -0500
Subject: [PATCH] Change to dge_vsm

---
 lessons/07_functional_analysis_pseudobulk.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lessons/07_functional_analysis_pseudobulk.md b/lessons/07_functional_analysis_pseudobulk.md
index c5e1c4d..38939aa 100644
--- a/lessons/07_functional_analysis_pseudobulk.md
+++ b/lessons/07_functional_analysis_pseudobulk.md
@@ -311,7 +311,7 @@ Now that we have run through functional analysis with the results from Pseudobul
 1. Create a significant DE genes data frame from the FM results with an added fold change criteria to reduce the gene list size. You can do this by running the code below:
 
 ```r
-sig_fc_dge <- dge_fm %>% dplyr::filter(p_val_adj < 0.05, abs(avg_log2FC) > 1)
+sig_fc_dge <- dge_vsm %>% dplyr::filter(p_val_adj < 0.05, abs(avg_log2FC) > 1)
 ```
 
 2. Use this gene list to run over-representation analysis. Be sure to separate genes into up- and down-regulated first. What are the top terms enriched among up-regulated genes? What are the top terms enriched among down-regulated genes?