Figure 2
From: A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
M-A plots of the perturbed data set using different normalization and reference selections. Top (A1-A3): invariant-set; middle (B1-B3): quantile; bottom (C1-C3): sub-array. Left column (A1, B1 and C1): the reference is the perturbed array Exp03_R1*; Middle column: the reference in both A2 and C2 is Exp03_R2, while the reference in B2 is the pseudo-reference defined as the average quantiles of all six arrays; Right column (A3, B3 and C3): the result obtained by the PTR method using all six arrays as references. The grey dots are non-spike-in genes; the black dots are spike-in genes which are expected to have log-ratio M = 1. We can see that the PTR method results are not affected by the perturbed array Exp03_R1* and offers the smallest variation for non-spike-in genes.