Current Analytical Methods of DNA Microarray Data - DNA Microarray Technology and Data Analysis in Cancer Research - page 24

Fig. 3.2. Boxplot of log 2 -transformed, RMA-processed probe intensities for all

samples.

Fig. 3.3. Boxplot of log 2 -transformed, iterPLIER-processed probe intensities for all

samples.

of the pairwise comparison will be calculated by permutation analysis
(1000 permutations) and adjusted for multiple testing using the false dis-
covery rate (FDR), q -value, method (Storey, 2002). Differentially
expressed genes are declared at an FDR q -value threshold of 0.05.