Analysis of high-throughput RNAi screening data in identifying genes mediating sensitivity to chemotherapeutic drugs: statistical approaches and perspectives

Table 1 Recommendation of analysis method based on simulation study

Number of replicates	Scenario	Noise	Drug effect	RNA effect	Performance ranking order*
3	1	low	strong	strong	LM, t, SI, FC
	2	moderate	strong	strong	LM, t, SI, FC
	3	strong	strong	strong	LM, t, SI, FC
	4	low	moderate	strong	LM, t, SI, FC
	5	low	weak	strong	LM, t, SI, FC
	6	moderate	weak	strong	LM, t, SI, FC
	7	strong	weak	strong	LM, SI, t, FC
	8	low	strong	moderate	LM, t, SI, FC
	9	low	strong	weak	LM, t, SI, FC
6	1	low	strong	strong	LM, t, SI, FC
	2	moderate	strong	strong	LM, t, SI, FC
	3	strong	strong	strong	LM, t, SI, FC
	4	low	moderate	strong	LM, t, SI, FC
	5	low	weak	strong	LM, t, SI, FC
	6	moderate	weak	strong	LM, t, SI, FC
	7	strong	weak	strong	LM, t, SI, FC
	8	low	strong	moderate	LM, t, SI, FC
	9	low	strong	weak	LM, t, SI, FC
9	1	low	strong	strong	LM, t, SI, FC
	2	moderate	strong	strong	LM, t, SI, FC
	3	strong	strong	strong	LM, SI, t, FC
	4	low	moderate	strong	LM, t, SI, FC
	5	low	weak	strong	LM, t, SI, FC
	6	moderate	weak	strong	LM, t, SI, FC
	7	strong	weak	strong	LM, t, SI, FC
	8	low	strong	moderate	LM, t, SI, FC
	9	low	strong	weak	LM, t, SI, FC
12	1	low	strong	strong	LM, t, SI, FC
	2	moderate	strong	strong	LM, SI, t, FC
	3	strong	strong	strong	LM, SI, t, FC
	4	low	moderate	strong	LM, t, SI, FC
	5	low	weak	strong	LM, t, SI, FC
	6	moderate	weak	strong	LM, t, SI, FC
	7	strong	weak	strong	LM, t, SI, FC
	8	low	strong	moderate	LM, t, SI, FC
	9	low	strong	weak	LM, t, SI, FC

* The ranking is based on average FNRs and FPRs of the methods: linear model (LM), t-test (t), sensitivity index (SI), and fold-change (FC).

ISSN: 1471-2164