Design and use of external controls in DNA microarray experiments Supplementary information for “In control: systematic assessment of microarray performance”

External RNA controls can be an important tool in determining microarray performance. External controls are synthetically produced RNA molecules with corresponding probes on the microarray. Control RNAs can be added to biological samples of interest in defined amounts. When spiked in at different levels between the two channels of a cDNA microarray, they can be used to assess the ability to detect differentially expressed genes (see accompanying paper). Other uses include normalization, sensitivity testing (Dorris et al., 2002; Girke et al., 2000; Hughes et al., 2001; Lockhart et al., 1996; Ramakrishnan et al., 2002; Relogio et al., 2002), background estimation (Dorris et al., 2002; Ramakrishnan et al., 2002), and the comparison of labelling strategies (Badiee et al., 2003). Detailed recommendations on how to design and handle external controls and corresponding microarray probes are described below.