Additional file 3.

Figure S3. Sensitivity of <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M20">View MathML</a> to hyper-parameter estimation. Scatter plot of <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M21">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M21">View MathML</a>, based on q1 = 0.8, q2 = 0.9 and q1 = .9, q2 = 0.95, respectively. The maximum difference in estimated fold change is less than 0.04, indicating that <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M20">View MathML</a> is not sensitive to the choice of q.

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Wu et al. BMC Bioinformatics 2010 11:564   doi:10.1186/1471-2105-11-564