Figure 1

Description of the evaluation study. Theevaluation study was based on raw data from eight Lucidea arrays (Figure 2). All arrays were scanned at four settings and image analysis was applied to extract raw data. The data were normalized in five steps. Filtration and background adjustment were applied to each of the raw data sets. Three procedures for filtration and two procedures for background adjustment were considered. In the third step, data from the four scans were "merged" together. Seven merging procedures were considered; four of these were single scan procedures that used only data from a single scan. Two procedures for channel adjustment and four censoring approaches were considered. In total, 252 unique analyses were conducted. For each analysis the normalized log-ratios were used to conduct a test that generated a list of genes classified as DE. Properties of the average normalized log-ratios and the analyses' classification properties were used to characterize and evaluate the analyses.