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Table 2 Average computation times for obtaining normalization factors

From: TCC: an R package for comparing tag count data with robust normalization strategies

P G1 50% 70% 90%
(a) TMM    
PDEG = 5% 0.13 0.18 0.22
PDEG = 15% 0.16 0.19 0.15
PDEG = 25% 0.17 0.14 0.15
(b) DEGES/TbT    
PDEG = 5% 1492.92 1423.55 1573.23
PDEG = 15% 1556.93 1510.17 1408.46
PDEG = 25% 1527.08 1483.09 1543.80
(c) DEGES/edgeR    
PDEG = 5% 3.04 3.08 3.24
PDEG = 15% 3.08 3.05 2.89
PDEG = 25% 2.99 2.92 3.05
(d) iDEGES/edgeR    
PDEG = 5% 8.80 8.95 9.53
PDEG = 15% 8.94 8.91 8.39
PDEG = 25% 8.75 8.39 8.92
(e) iDEGES/TDT    
PDEG = 5% 17.92 17.54 18.24
PDEG = 15% 19.85 19.45 18.74
PDEG = 25% 21.17 20.74 21.16
(f) iDEGES/DESeq    
PDEG = 5% 17.88 17.54 18.34
PDEG = 15% 19.96 19.43 18.72
PDEG = 25% 21.17 20.75 21.27
  1. Average computation times (in seconds) of 100 trials for the six normalization methods in Table 1 are shown. The results of DEGES/TbT were obtained by using a suggested parameter setting for performing bootstrap resampling (i.e., samplesize = 10000).