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Table 3 Description of data sets

From: Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments

Data set

m(% of genes with only zero counts)

\(n_1/n_2\)

Description

Kidney

20531 (3)

72/ 72

non-tumour versus tumour samples [6]

Kidney 2

20531 (5)

10/10

random sample of Kidney data set

Bottomly

36536 (35)

10/11

C57BL/6J versus DBA/2J (mice strains) [7]

Mouse mammary

27179 (21)

6/6

basal versus luminal cell types in mice [10]

Sultan

52580 (83)

2/2

human embryonic kidney versus B cell lines [8]

Airway

64102 (52)

4/4

Airway smooth muscle cell lines [19]

Airway 2

64102 (52)

2/2

random sample of Airway data set [19]

De novo assembly:

 

\(n_1/../n_4\)

 

Yuen

96831 (12)

3/3/3/3

transcriptomes of lucinid clam of 4 organs [20]

Only data simulation:

 

\(n_1\)

 

Cheung

52580 (76)\(^1\)

41

lymphoblastoid cell lines from unrelated

   

individuals [11]

  1. \(^1\) only a subset of 17580 genes with a reduced percentage of genes with only zeros is used for data simulation