Original Permuted
Treatment Condition log2 CPM Treatment Condition log2 CPM
A M 5.0 A N 5.0
A M 10.0 B M 10.0
A N 2.5 B M 2.5
A N 2.0 A N 2.0
A N 3.0 A M 3.0
B M 1.5 B N 1.5
B M 2.0 A N 2.0
B N 7.0 B M 7.0
B N 6.5 A N 6.5
Table 3: Example of how permutation of experimental design is conducted. Experimental treatment labels are permuted, which breaks any association with expression. Any patterns seen in these permuted data sets is consistent with random variability.