Output of Seurat FindAllMarkers parameters I compared two manually defined clusters using Seurat package function FindAllMarkers and got the output:



Now, I am confused about three things:


What are pct.1 and pct.2?
How come p-adjusted values equal to 1? What does it mean?
If we take first row, what does avg_logFC value of -1.35264 mean when we have cluster 0 in the cluster column? Is it that in cluster 0 the Cttnbp2 gene downregulated by a factor of 2^1.35264?
pct.1– The percentage of cells where the gene is detected in the first group
p_val_adj– Adjusted p-value, based on bonferroni correction using all genes in the dataset. This is also known as a false discovery rate (FDR) adjusted p-value. An adjusted p-value of 1.00 means that after correcting for multiple testing, there is a 100% chance that the result (the logFC here) is due to chance.
You are correct. The expression of Cttnbp2 donwn-regulated by that factor. If you were to look in the table at the cluster 1 DE genes you would see Cttnbp2 with a logFC value of 1.35264. When you are looking at genes differentailly expressed in only two clusters, the sign is the only thing that changes.


Vignette posted above by @heathobrien.