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Table 3. Number of probe sets showing signal intensity differences between human and chimpanzee tissues in the oligonucleotide arrays by using several analysis methods

Several normalization and analysis methods were used to identify the probe sets showing signal intensity differences in the oligonucleotide arrays in four different comparisons of human and chimpanzee tissues: cerebral cortex (this work and analysis of data from ref. 1), heart (this work), and liver (analysis of data from ref. 1). Array data were analyzed with three programs: MICROARRAY SUITE (MAS), Ver. 4.0 (Affymetrix); BULLFROG, Ver. 4.5 (2); DCHIP, Ver. 1.0 and 1.1 (3); and TERAGENOMICS (Information Management Consultants, www.teragenomics.com). In the MAS and BULLFROG analyses, the arrays were normalized to the same average intensity on the basis of all probe sets excluding the 10% with the highest and the 60% with the lowest hybridization signals (10–60% normalization) or excluding the 2% with the highest and the 2% with the lowest hybridization signals (2–2% normalization). In the DCHIP analysis, all arrays were normalized to the same overall intensity on the basis of the invariant set of probes. Three different ways to calculate the gene expression values were used (3): average difference, Perfect Match/Mismatch (PM/MM) difference model, and Perfect Match (PM) only model. The total number of probe sets showing signal differences between humans and chimpanzees obtained with each analysis method is indicated in the table, together with those with higher intensities in humans than in chimpanzees (Up) and with lower intensities in humans than in chimpanzees (Down). In all cases, a clear skewing toward higher hybridization levels in humans than in chimpanzees for the majority of genes with signal differences was observed in the cortex, but not in heart or liver.

*Includes the combination of the probe sets identified with the MAS + BULLFROG 10–60% normalization analysis and the DCHIP average difference analysis: cerebral cortex (this work), 157 exclusive to MAS + BULLFROG, 16 exclusive to DCHIP, and 73 in common to both; cerebral cortex (1), 114 exclusive to MAS + BULLFROG, 101 exclusive to DCHIP, and 96 in common to both; heart (this work), 637 exclusive to MAS + BULLFROG, 25 exclusive to DCHIP, and 179 in common to both; liver (1), 121 exclusive to MAS + BULLFROG, 181 exclusive to DCHIP, and 219 in common to both.