Figure 1

Boxplots of the distributions of the inter-slide, intra-cell line log₂-ratios (y axis) calculated between cell line replicate pairs are shown in A (white: BattP12; yellow: Jurkat; green: MCF7, pink: REF). All pair-wise comparisons for each platform are shown. To the right is a summary (minimum (min %) and maximum (max %)) of the relative number of targets having a fold change superior to 2 (-1.0 > log₂-ratio > 1.0) between replicate samples. B shows the box plots of the distributions of the average inter-array, intra-cell line variation measured as the coefficient of variation (CV) measured for the log₂ intensities (Amersham and Affymetrix) or standard deviation (SD) of log₂-ratios (Amersham (Amer.), Affymetrix (Affy.) and Agilent). To the right is a table of the 50^th (median) and 95^th percentile values obtained from different measures of variation between replicate slides (SD of log₂-ratios and CV of log₂-intensities). Minimum (dotted lines) and maximum (filled lines) intra-quantile correlation of expression values for each platform are shown in C. The values were based on log₂-ratios. All correlation coefficients (Pearson correlation coefficient plotted on the y-axis) were calculated for all pair-wise comparisons between replicates data for the same cell line. Quantile attribution was based on the median intensities across all cell lines for a given platform where Q1 = lowest 25% mean intensities targets and Q4 = the 25% highest mean intensities targets (see Methods). Color code is as follows: green: Affymetrix; red: Amersham; black: Agilent.