1. RNA sample quality: As described in this manual, the quality of starting RNA is very important. Ratio of 260/280 absorbance values, as well as appearance of samples by gel electrophoresis, are suggest methods to detect any degradation of your RNA samples.

2. Target labeling: Various QC protocols described in this manual can be employed at different stopping points of the assay. For example, gel electrophoresis after cDNA synthesis (if using poly-A mRNA as starting material), after cRNA synthesis, and after fragmentation is helpful in estimating quantity and size distribution. Spectrophotometric measurements are also important after cRNA synthesis. Low cRNA yield can be a sensitive indicator of problematic labeling procedures and/or starting material. You may also want to experiment with using real-time PCR analysis on house-keeping genes after each of these reactions to monitor the efficiency of each step.