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Table 5 Rankings of methods by the mean squared error of false discovery rates under variable library factors

From: A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

Method

#DE = 100

#DE = 1000

#DE = 2000

 

1.5 FC

2 FC

4 FC

1.5 FC

2 FC

4 FC

1.5 FC

2 FC

4 FC

tweeDEseq

2

2

1

1

1

1

1

1

4

DESeq - PgOn

4

4

4

3

3

5

2

4

8

DESeq - Pmax

1

3

2

7

7

7

8

8

5

DESeq - CgOn

9

9

9

9

9

9

9

9

9

DESeq - Cmax

3

1

3

2

2

2

5

5

1

edgeR - (def)

7

7

7

6

6

6

6

6

6

edgeR - QLF (def)

6

6

6

5

5

4

4

3

2

edgeR - Df1

8

8

8

8

8

8

7

7

7

edgeR - QLF Df1

5

5

5

4

4

3

3

2

3

  1. Data in this table correspond to the rankings of every method by the mean squared error (MSE) values shown in Table 2.
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BMC Bioinformatics

ISSN: 1471-2105

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