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).

Ye et al. BMC Genomics 2012 13(Suppl 8):S3   doi:10.1186/1471-2164-13-S8-S3

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