Hello Michael Love ,
I used DESeq2 to find DE genes between 2 groups in our dataset. Now, I'm trying to see if the number of DE genes is significant. So I repeated the following steps many times:
- permute the sample labels (i.e. column names)
- run DESeq2 on the permuted dataset
- Get the number of DEG
This generated a distribution of DEG. However, the true number of DEG is not significant compared to this distribution. Did I do the permutation test correctly, or is there another way to determine whether the number of DEG is significant? Is the permutation test even necessary?
For context, the dataset contains 6 groups (3 conditions in 2 tissues). I'm trying to compare 2 conditions in a single tissue.
Thank you for the help!