Table 3. Between-batch variation as measured by average number of DEGs (standard deviations where N>3).

Species/sample condition	Experiment	Sampling Date	Scan Date	RNA Date	RNA Person
PPR	4517 (889)	4312 (1009)	4640 (1616)	4667 (941)	5872 (2045)
DRE	2523 (1651)	2841 (2141)	6321	5503	3669

The DEGs were identified in paired comparisons of N–1 batches against a batch designated as a common reference. N is the total number of batches in a factor. The comparisons were made in conjunction with the analysis of within-batch effects involving 250 permutations. There were little variations in between-batch effects among permutations so their calculations were made only from the first permutation. DRE, zebrafish; PPR, fathead minnow.