Output of Seurat FindAllMarkers parameters
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.