not centered volcano plot, Seurat
Hello.
I performed DE analysis on single cell data using Seurat, following the pseudobulk tutorial on this page. After DE analysis, I drew a volcano plot, and the result is a non-centered volcano plot.
The center of the volcano plot is not located at 0 on the x-axis. I looked into the reason for this and found that this problem occurs when there is a problem with fc.slot when analyzing using the FindMarkers() function in Seurat, but I couldn't find a proper solution. How can I solve this problem? I used Seurat v.5.
Please help me. Thank you for help!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Differential expression analysis between groups with varying cell proportions
written by AB
-
Volcano Plot and DGE analysis
written by JuanJo •
-
Pseudobulking per patient
written by bio_info •
-
GO analysis: Indicate genes corresponding to the pathway
written by sooni •
-
GO analysis: p-value range
written by sooni •
-
ggrepel function: geom_text_repel()
written by sooni •
-
Spatial transcriptome analysis
written by siu
-
Single cell DEG analysis. Wildly different results from different FindMarkers test
written by jevanveen •
-
Confusion about FindMarkers(), FindVariableFeatures(), RunTSNE(), and RunUMAP() in seurat package
written by Farah
-
How to plot motif footprint?
written by tamadomi •
My suggestions would be to plot an MA-plot first, and show this. Usually non-centered plots indicate poor normalization. Which test did you run?
I ran DESeq2 as a test! Bottom line is, I solved this problem! It was caused by creating pseudo-bulk data and not running the
NormalizeData()function. This problem is now solved.