I am having trouble understanding the avg_logFC results of an integrated dataset (control and condition) in Seurat (3.1) for the FindMarkers pipeline.
gene_name p_val avg_logFC pct.1 pct.2 p_val_adj
gene1 0 -0.270265934 1 0.115 0
gene2 0 -0.332681178 1 0.167 0
gene3 7.25E-119 0.251635681 0.855 0.238 1.45E-115
gene4 2.10E-86 0.255847237 0.856 0.293 4.19E-83
gene5 2.84E-76 0.257140547 0.923 0.399 5.68E-73
pct.1 represents control in cluster1 and pct.2 represents condition in cluster 1.
According to Seurat vignettes - avg_logFC : log fold-chage of the average expression between the two groups. Positive values indicate that the feature is more highly expressed in the first group
What about negative values? For gene 1, avg_logFC is -0.2. Does that mean gene 1 is downregulated in control group in cluster 1? But why is percentage of cells expressed in gene1 more in control cells than condition cells?
Am I missing something?