Current Analytical Methods of DNA Microarray Data - DNA Microarray Technology and Data Analysis in Cancer Research - page 22

Table 3.1. Experimental design. Note that Mut_A_1 or Mut_A_2, B6_1 or B6_2, and
Vector_1 or Vector_2 are names of the RNA samples for DNA microarray experiment.

Array Strain Strain_Rep Sample Dye

GC_Gene1.0ST_GES08_0064_040208_1 Mut_A Mut_A_1 1 1

GC_Gene1.0ST_GES08_0065_040208_1 B6 B6_1 2 1

GC_Gene1.0ST_GES08_0066_040208_1 Vector Vector_1 3 1

GC_Gene1.0ST_GES08_0067_040208_1 B6 B6_2 4 1

GC_Gene1.0ST_GES08_0068_040208_1 Mut_A Mut_A_2 5 1

GC_Gene1.0ST_GES08_0069_040208_1 B6 B6_3 6 1

GC_Gene1.0ST_GES08_0070_040208_1 Vector Vector_2 7 1

GC_Gene1.0ST_GES08_0071_040208_1 B6_P210 B6_P210_1 8 1

variance components from within the R/maanova package (Cui et al .,
2005; Wu et al ., 2003). Statistical significance levels of the pairwise com-
parison will be calculated by permutation analysis (1000 permutations)
and adjusted for multiple testing using the false discovery rate (FDR),
q -value, method (Storey, 2002). Differentially expressed genes are declared
at an FDR q -value threshold of 0.05.

3.2.2 . iterPLIER

Average signal intensities for each probe set within arrays were calculated
by and exported from Affymetrix's Expression Console (Version 1.1)
software using the iterPLIER method with background adjustment (PM-
GCBG). These values were read into R/maanova; a value of 16 was added
to the processed probeset intensities to account for iterPLIER's zero-
based method, log-base-2-transformed, and quantile-normalized to equal-
ize the distribution of intensities across all arrays. For this experiment,
three pairwise comparisons will be used to statistically resolve gene
expression differences between strain groups using the R/maanova
analysis package (Wu et al ., 2003). Specifically, differentially expressed
genes will be detected by using F s , a modified F -statistic incorporating
shrinkage estimates of variance components from within the R/maanova
package (Cui et al ., 2005; Wu et al ., 2003). Statistical significance levels