Platform specific performance characteristics in view of ERCC spike-ins

RNA-Seq provides an exciting new approach for semi-quantitative expression profiling. On one hand, expression estimates do not suffer non-linear effects like dye-based platforms such as typical microarrays. On the other hand, expression estimates for less strongly expressed genes are very noisy due to the sampling effects seen in count-based methods. We here compare the response characteristics of RNA-Seq and a modern custom microarray using External RNA Control Consortium (ERCC) spike-ins. ERCC spike-ins were added to mRNA samples in known ratios and abundances. Platform specific response characteristics can then be studied in an analysis of the signal response in a comparison to the expected values. We can show that at sufficiently high expression levels, the expected ratios are accurately and precisely recovered for RNA-Seq. For microarrays, non-processed signals show non-linear saturation effects. Application of modern signal models, however, allow a correction for these technical effects, yielding results matching RNA-Seq in accuracy and precision. It is noteworthy that the compared platforms behave very differently for lower expression levels. As expected from theory, RNA-Seq suffers from strong sampling effects whereas microarrays show an attenuated signal response for weakly expressed genes.