I was wondering which is the criteria to set the minimum counts that a gene is considered for further analysis when doing DE between control and treated samples. Is there any way to change this threshold to be more stringent? One I analyze my data set, if I use the default setting I get 1400 genes that are DE. However if I delete all genes that have an average count < 10 from the count matrix I do only get 300 DE genes. Is there an arbitrary way to select the genes that have a reasonable minimun counts?