. Author manuscript; available in PMC: 2014 Feb 1.

Published in final edited form as: Nat Protoc. 2013 Jul 11;8(8):10.1038/nprot.2013.084. doi: 10.1038/nprot.2013.084

Table 3.

Example contents of logarithmic vs. plateau growth edgeR ‘DE_results’ file

Transcript	logFC	logCPM	PValue	FDR
comp5128_c0_seq1	10.3	11.1	2.13e-22	1.22e-18
comp5231_c0_seq1	10.0	10.9	1.10e-21	3.13e-18
comp5097_c0_seq1	8.7	11.3	5.72e-20	1.10e-16
comp1686_c0_seq1	9.2	10.4	1.01e-19	1.46e-16
comp1012_c0_seq1	8.3	11.5	2.8e-19	3.23e-16

logFC: log₂(fold change) = log₂(plateau_phase/logarithmic_growth)

logCPM: log₂(counts per million)

FDR: false discovery rate