a) Dose response curve showing cRNA yield from the first round RT-IVT amplification as a function of total RNA input for Jurkat total RNA sample from FF or for a colon carcinoma RNA derived from FFPET. b) Plot showing the distribution of cRNA yield from the first and second round RT-IVT amplifications from a representative set of FFPET samples. First round and second round yields are shown as black diamonds and blue squares, respectively. The first round RT input is 100 ng and second round RT input is 500 ng. c) One-dimensional heatmap of hybridization experiments starting with the same total RNA but with different mass input, showing that both the first and second round can tolerate more than 2-fold of sample mass imbalance. The left panel bar graph shows the number of significant signatures, and the right panel heatmap shows total number of genes selected for these analysis.