Could I consider an ENCODE experiment with two library as two replicates for differential analysis?

Question

[zau saa]

Hi! I'm searching data in database for differential analysis and I found some ENCODE experiments have two libraries. Though they are merged for peak calling in ENCODE project, could I consider it as two replicates?

Answer 1

[i.sudbery]

No, these are technical, not biological replicates. Differential expression analysis expects replicates to follow a negative binomial distribution, by these would follow a poisson distribution. If you want to make some statement about, say "Thoracic aorta" chromatin openness differing, in general, from some other tissue (say heart), you need to know about the variation from person to person. If, say your heart tissue came from another individual, how would you know whether any difference between them was due to coming from different tissues, rather than, say different individuals, without a measure of how chromatin accessibility varied from person to person.

Even in the same individual, how would you be able to distinguish between differences due to tissue, from differences due to one being done on a tuesday and the other on wednesday.

[zau saa]

Thank you for your detailed statement, much appreciated!