Figure 4.

Shrinkage estimate of log fold change. Shrinkage estimate of log fold change from ASC plotted against apparent log fold change for all genes. The apparent log fold change is defined as <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M2">View MathML</a> where x* = x ∧ 0.5 to avoid logarithm of 0 counts. The darkness of each point reflects the average rpm, <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M3">View MathML</a>, of a gene, with the darkest being the highest average rpm. The straight line is the identity line representing no shrinkage. The genes with lighter gray have lower average rpm and are shrunk more.

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