Computational Drug Discovery and Design

4 Notes

1. The quality of RNA can be measured by 3^0 –5^0 ratio or 3^0 to mid
   ratio if the RNA is prepared by Affymetrix Standard Protocol
   and Affymetrix Small Sample protocol, respectively. If 3^0 –5^0
   ratios for β-actin and GAPDH are used, the parameter
   usemid¼Tshould be removed during quality control.
   2.jActiveModulesapplies the Monte Carlo algorithm for random
   sampling, suggesting that the results may not be the same in
   different runs. It is worthwhile to repeatjActiveModulesseveral
   times to identify reproducible modules across runs.


2. In correlation analysis, "pearson" is the default method in
   psychpackage. Alternatives are "spearman" and "kendall".
   The adjustment methods include the Bonferroni correction
   ("bonferroni") in which the p-values are multiplied by the
   number of comparisons. Less conservative corrections include
   Holm (1979) ("holm"), Hochberg (1988) ("hochberg"),
   Hommel (1988) ("hommel"), Benjamini & Hochberg
   (1995) ("BH" or its alias "fdr"), and Benjamini & Yekutieli
   (2001) ("BY").

Fig. 12(continued)

194 Sze Chung Yuen et al.