Table 3

Summary of the parameters used to generate the synthetic data sets
Sim. study

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|{g;ϕg = 0}| ‘Single’ outlier fraction ‘Random’ outlier fraction

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0 0 0 0 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M59','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M59">View MathML</a>

1,250 0 0 0 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M60','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M60">View MathML</a>

625 625 0 0 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M61','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M61">View MathML</a>

4,000 0 0 0 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M62','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M62">View MathML</a>

2,000 2,000 0 0 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M63','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M63">View MathML</a>

0 0 6,250 0 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M64','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M64">View MathML</a>

625 625 6,250 0 0

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0 0 0 10% 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M66','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M66">View MathML</a>

625 625 0 10% 0

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M67','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M67">View MathML</a>

0 0 0 0 5%

<a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M68','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M68">View MathML</a>

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 <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M54','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M54">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M55','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M55">View MathML</a> 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; ϕg = 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., <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M56','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M56">View MathML</a>, in the superscript) and the number of DE genes that are downregulated in S2 (i.e., <a onClick="popup('http://www.biomedcentral.com/1471-2105/14/91/mathml/M57','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/14/91/mathml/M57">View MathML</a>, in the subscript).

Soneson and Delorenzi

Soneson and Delorenzi BMC Bioinformatics 2013 14:91   doi:10.1186/1471-2105-14-91

Open Data