Principal components analysis plots. (A) Fresh-frozen tissue, (B) Formalin-fixed, paraffin-embedded tissue (FFPET) samples processed using the NuGEN RNA amplification kit, (C) FFPET samples processed using the Affymetrix Two-Cycle RNA amplification kit, and (D) FFPET samples processed using the Sigma/Rubicon Genomics RNA amplification kit. Note the extremely similar shape of fresh-frozen and FFPET data clusters associated with the NuGEN workflow. The NuGEN kit also provides the most parsimonious description: in order to capture the effect of estrogen receptor (ER) status on gene expression, both the Two-Cycle and the Sigma/Rubicon Genomics kit would require at least two leading principal components. Circles and triangles represent ER– and ER+ samples correspondingly. Technical replicates are shown in red.