I was trying to analyze my NGS data with DESeq package and have couple of questions with the same. Could you help me in answering these problems.
- After I apply nbinomTest, I get P values in range of 0-1. And fold changes of greater and lesser than 1.5. Assuming these as up and down-regulated how do you interpret P values for them. If the fold change is greater than 1.5 than it’s an upregulated gene what should be its expected P value (Normally if P value is less than 0.05 it’s significant but in my case all the P values are between 0-1).
- If I look at the adjusted P values for them most of them are equal to 1. So am confused if there is an up or down regulated gene which P value is significant and how do I report them in paper.