Figure 6
Comparison of differential gene expression data using Affymetrix one-round and Nugen chemistries. Targets were generated from RNAs of two cell lines using Affymetrix 1-round IVT and Nugen chemistries. After hybridisation, differential gene expression results were normalised (MAS5) and the expression ratio calculated for each probeset. Logarithm of ratios to the base 2 (Log2 ratios) were computed for each chemistries and graphed(X axis Nugen and Y axis Affymetrix). Differences in the direction of differential expression were only observed for 4% of the probesets (dots located in the upper-left quadrant and lower-right quadrant). Moreover, almost all of those probesets show a low differential expression (absolute value lower than 1, less than 2-fold over or lower expression). The slope of the regression line is 1.033 (p < 10-16) and it intercepts the Y axis at -0.02 (p < 10-12). The Pearson's correlation coefficient has been calculated between the expression ratios distribution (R = 0.321).