Figure 5

Comparison of microarray and quantitative RT-PCR results for genes of NF-κB pathway. Scatter plots of MAS5.0 scaled probe set intensities measured on the GeneChip Human Genome Focus Array and real-time PCR ΔCt values for 75 genes of the NF-κB pathway. A. Sample C, microarray targets prepared with Method 1; B. Sample C, microarray targets prepared with Method 2; C. Sample C, microarray targets prepared with Method 3; D. Sample C, microarray targets prepared with Method 4. Microarray data was analyzed and scaled with MAS 5.0 and RT-PCR data was normalized by subtracting the mean Ct value for five housekeeping genes (β₂-microglobin, hypoxanthine phosphoribosyltransferase 1, ribosomal protein L13a, glyceraldehyde-3-phosphate dehydrogenase, and β-actin) to yield ΔCt values. Pearson correlation coefficients are reported for each comparison.