Table 1.

Summarized metrics for analyzed pipelines based on an experimental dataset

Method	SD low	SD medium	SD high	NE (K = 1)	NN (K = 1)	TxDiff low	TxDiff medium	TxDiff high	deFC low	deFC medium	deFC high	pAUC
Cufflinks	0.62 (0.002)	0.26 (0.001)	0.12 (0.000)	0.08	0.70	0.31 (0.007)	0.08 (0.002)	0.03 (0.001)	2.65 (0.022)	2.25 (0.047)	1.01 (0.024)	0.77
eXpress	0.53 (0.002)	0.22 (0.001)	0.10 (0.000)	0.07	0.72	0.24 (0.006)	0.06 (0.002)	0.02 (0.001)	2.86 (0.022)	2.21 (0.048)	1.00 (0.019)	0.79
Flux Capacitor	0.62 (0.003)	0.57 (0.003)	0.18 (0.001)	0.10	0.73	0.42 (0.008)	0.15 (0.004)	0.07 (0.003)	2.62 (0.024)	2.40 (0.050)	1.01 (0.025)	0.75
kallisto	0.53 (0.002)	0.24 (0.001)	0.12 (0.000)	0.09	0.64	0.28 (0.007)	0.08 (0.002)	0.03 (0.0001	2.36 (0.024)	2.06 (0.045)	1.03 (0.024)	0.76
RSEM	0.54 (0.002)	0.22 (0.001)	0.11 (0.000)	0.06	0.73	0.39 (0.008)	0.07 (0.002)	0.02 (0.001)	2.72 (0.022)	2.22 (0.048)	1.03 (0.026)	0.78
Sailfish	0.46 (0.002)	0.25 (0.001)	0.13 (0.000)	0.08	0.60	0.27 (0.006)	0.08 (0.002)	0.04 (0.001)	2.30 (0.023)	2.08 (0.044)	0.97 (0.022)	0.77
Salmon	0.46 (0.002)	0.23 (0.001)	0.12 (0.000)	0.08	0.65	0.29 (0.007)	0.07 (0.002)	0.04 (0.001)	2.30 (0.024)	2.06 (0.045)	1.03 (0.022)	0.77

Metrics for single cell lines are averaged for both cell lines, except standard deviation is the square root of average squares. Columns 2–4 shows median standard deviation on three transcript abundance levels; column 5 shows proportions of discordant calls when K = 1; column 6 shows proportions of both non-expressed when K = 1; columns 7–9 show the mean proportion differences of transcripts in genes only having two annotated transcripts based on three transcript abundance levels; columns 10–12 show median log fold changes of true differentially expressed genes based on three abundance levels; column 13 shows standardized partial area under the curve for differential expression of genes. pAUC partial area under the receiver operating characteristic curve