EnhancedVolcano underrepresenting DEGs

I'm plotting my DEGs from DESeq2 with EnhancedVolcano, but I can see that not all genes that have LFC > 1 or < -1 are shown in the plot. The number of red dots on the plot is clearly lower than the number of genes. Does anyone know what might be the reason?

• 737 views • link

updated 2.7 years ago by Kevin Blighe

• written 2.7 years ago by jabbari.parnian •

results %>%
  ggplot(aes(x=log2FoldChange, y=-log10(padj))) +
  geom_point()

Use that to inspect your data, everything else is eye-candy. Confirm with this that you're seeing what you expect.

• 0 views • link

written 2.7 years ago by ATpoint

0 answers

No answers yet.

More posts like this

Pathview modifies LFC genes. Is this normal?
written 2.5 years ago by Alex •

Hello everyone, I recently found out that when I analysing KEGG pathways and visualizing them using Pathview, genes with a different LFC indicator, different from …
How to label genes passing the p-value and fold change cut-offs in EnhancedVolcano?
written 4.3 years ago by mohammedtoufiq91

Hi, I have question on labelling of genes. I am interested to know if there is a way to label genes passing the p-value (purple …
Strange patterning in volcano plot
written 4.4 years ago by Kathryn •

Hi all, I made a volcano plot from my DEseq2 output (DE on bulk RNAseq), and it has this weird "stripy" patterning. Does anyone know …
Higlight a dot in a volcano plot using EnhancedVolcano
written 4.7 years ago by santiagoboccardo31 •

Hi, I have been using enhanced volcano tool to construct a volcano plot of DEGs between two conditions. I could construct the volcano plot and …
Deseq2 Result
written 4.8 years ago by Diango •

I use Deseq2 to perform differential gene expression analysis. I have successively changed the LFC, i.e.LFC > 1.5 and LFC > 2 as shown in …
Color layer in ggplot (Volcano plot)
written 4.9 years ago by arsa •

I'm trying to plot a volcano plot with ggplot's vplot. My issue is that I want the colored dots on the front layer rather than …
Plotting points that are in Enhanced Volcano that are 0.01 LFC units apart
written 5.3 years ago by raisamathenge •

Hello! Does anyone know if enhanced volcano can be used to plot genes that have LFC values that are 0.01 units apart or does anyone …
What result from DESeq2 should be used as an input for volcano plot?
written 6.1 years ago by helen •

My cutoff for differentially expressed genes (DEGs) is **adjusted *P* < 0.05** and **|log2FoldChange| > 1**. I used this code in DESeq2 to get those …
Differential expression tool that can take TPM as input?
written 6.7 years ago by Tye Kahn •

Due to my analysis, I need to use TPM as input for my differential expression analysis. I tried to use both DESeq2 and EdgeR by …
Showing FDR and log2FC in Volcano plot using R
written 8.7 years ago by Farbod

Dear Biostars, Hi In order to bioinformaticly show DEGs of RNA-seq in a volcano plot, I intend to use R, showing DEGs with **blue** spots …