Sim. study
|
|
|
|{g; ϕ
g
= 0}|
|
‘Single’ outlier fraction
|
‘Random’ outlier fraction
|
---|
|
0
|
0
|
0
|
0
|
0
|
|
1,250
|
0
|
0
|
0
|
0
|
|
625
|
625
|
0
|
0
|
0
|
|
4,000
|
0
|
0
|
0
|
0
|
|
2,000
|
2,000
|
0
|
0
|
0
|
|
0
|
0
|
6,250
|
0
|
0
|
|
625
|
625
|
6,250
|
0
|
0
|
|
0
|
0
|
0
|
10%
|
0
|
|
625
|
625
|
0
|
10%
|
0
|
|
0
|
0
|
0
|
0
|
5%
|
|
625
|
625
|
0
|
0
|
5%
|
- In all synthetic data sets, the observations were distributed between two conditions (denoted S1 and S2), with the same number of observations (2, 5 or 10) in each condition. We let and denote, respectively, the number of genes that were up- and downregulated in condition S2 compared to S1. The number of genes whose counts were drawn from a Poisson distribution (i.e., with the dispersion parameter equal to zero) is given by |{g; ϕ
g
= 0}|. The ‘single’ outlier fraction denotes the fraction of the genes for which we selected a single sample and multiplied the corresponding count with a factor between 5 and 10. The ‘random’ outlier fraction denotes the fraction of counts that were selected randomly (among all counts) and multiplied with a factor between 5 and 10. The notation for the simulation studies (leftmost column) summarizes the type of simulation (B - ‘baseline’, P - ‘Poisson’, S - ‘single outlier’, R - ‘random outlier‘), the number of DE genes that are upregulated in S2 (i.e., , in the superscript) and the number of DE genes that are downregulated in S2 (i.e., , in the subscript).