Entering edit mode
8 weeks ago
Chris ▴ 70
Good morning all,
In RNA-Seq, we use a raw count matrix to create a volcano plot, so which data and how we can generate a volcano plot from a scRNA-Seq experiment? I use Seurat but don't know how to extract the data used as input for
EnhancedVolcano(). I don't see the row as gene ID and the column as the cell 😅. Thank you so much!
A Volcano plot visualizes logFC vs -log10p(pvalue). You just need results from a differential analysis. Can you elaborate more which analysis you're doing and which step you're at.
I follow the instruction on several tutorials, to the end of the analysis and use
FeaturePlot()to find genes differently express between 2 conditions and want to make
It would be useful if you provide the code you executed to perform the differential analysis, otherwise it is difficult to know the format of the objects you created
I am sorry that it is pretty long but I think it is easier to help answer the question.
"p_val" for nominal p-values but "p_val_adj" could be used for adjusted p-values
Thank you for your help! I got an error that I could not find the solution on the Internet:
Loading required package: ggrepel Error in value[3L] : Package ‘ggrepel’ version 0.9.2 cannot be unloaded: Error in unloadNamespace(package) : namespace ‘ggrepel’ is imported by ‘Seurat’ so cannot be unloaded
Could you have a suggestion?
Update. I figured it out.