What controls are used in the analysis?
The quality of the starting RNA samples will be confirmed using the Agilent BioAnalyzer. We recommend adding internal “spiked” controls to the RNA samples before cDNA synthesis. The control RNAs come with the Affymetrix kit and provide a means of controlling for variations in cDNA synthesis or probe labeling. A biotinylated oligonucleotide is always included as a hybridization control. After hybridization, several quality control methods, including evaluation of scaling factors, comparison of 5’ to 3’ labeling ratios, the percentage of ‘Present’ calls and the expression of internal and ‘spiked’ controls, will be used to validate the quality of the microarray data. Any samples that fail to pass the stringent quality control measures will be identified and eliminated before the analysis.
