Table 2

Comparison of methods.

Evaluation

Cuffdiff

DESeq

edgeR

limmaVoom

PoissonSeq

baySeq


Normalization and clustering

All methods performed equally well

DE detection accuracy measured by AUC at increasing qRT-PCR cutoff

Decreasing

Consistent

Consistent

Decreasing

Increases up to log expression change ≤ 2.0

Consistent

Null model type I error

High number of FPs

Low number of FPs

Low number of FPs

Low Number of FPs

Low number of FPs

Low number of FPs

Signal-to-noise vs P value correlation for genes detected in one condition

Poor

Poor

Poor

Good

Moderate

Good

Support for multi-factored experiments

No

Yes

Yes

Yes

No

No

Support DE detection without replicated samples

Yes

Yes

Yes

No

Yes

No

Detection of differential isoforms

Yes

No

No

No

No

No

Runtime for experiments with three to five replicates on a 12 dual-core 3.33 GHz, 100 G RAM server

Hours

Minutes

Minutes

Minutes

Seconds

Hours


AUC, area under curve; DE, differential expression; FP, false positive.

Rapaport et al. Genome Biology 2013 14:R95   doi:10.1186/gb-2013-14-9-r95

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