By turning off the cook's cutoff I was able to obtain a p-value for all the genes that have a p-value from DESeq and EdgeR but not from DESeq2. However, I also notice something interesting: Some of the genes have a different p-value before and after turning off the Cook's Cutoff (The change was small though)
using mcols shows that all the values are the same. I guess the difference is not that big so it should be fine.
using mcols shows that all the values are the same. I guess the difference is not that big so it should be fine.
Code:
On Off 2.0392E-06 1.91466E-06 6.24279E-06 5.89022E-06 3.3727E-06 3.17301E-06 8.30502E-06 7.83552E-06 2.62679E-06 2.46954E-06 3.31702E-06 3.11984E-06 5.42979E-06 5.11889E-06 2.6574E-06 2.49848E-06 3.11848E-06 2.93252E-06 1.50445E-05 1.42226E-05 5.14826E-06 4.85033E-06 2.46503E-06 2.31563E-06 3.11574E-06 2.92985E-06 3.64453E-06 3.43143E-06
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