Hello,

I am analyzing scRNAseq data by using seurat pipeline. I have two simple question. As per Satija lab tutorial,

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.

pct.1: The percentage of cells where the feature is detected in the first group

pct.2: The percentage of cells where the feature is detected in the second group

1. Then does the negative value of avg_logFC mean the feature is more highly expressed in the second group?

2. I have loaded samples such as 1st control and then 2nd treatment. by using Read10x function. In order find gene expression cluster19 between control and treatment, I ran the following code. So, in this analysis pct1 belongs to which group (treatment or control)?

   cluster19.markers <- FindMarkers(Disease.combined, ident.1 = 19, min.pct = 0.25)

Could you please help me with this question? Thank you so much in advance.