Current Analytical Methods of DNA Microarray Data - DNA Microarray Technology and Data Analysis in Cancer Research - page 21

CHAPTER 3
Current Analytical Methods of DNA
Microarray Data
Analysis of DNA microarray data includes multiple steps. Here, we
describe some general procedures for the analysis, using our microarray
data discussed in Table 3.1 as an example.
3.1. Experimental Design
This experiment had one factor, Strain , a fixed factor with three levels
( B6 , Mut A , and Vector with 3, 2, and 2 biological replicates, respectively).
A total of eight Affymetrix Mouse Gene 1.0 ST Arrays were used for gene
expression analysis (Table 3.1).
3.2. Method
3.2.1. Robust multi-chip averaging ( RMA)
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 RMA method, which incorporates convolution back-
ground correction and a summarization based on a multi-array model fit
robustly using the median polish algorithm. These values were read into
R/maanova and quantile-normalized. For this experiment, three pairwise
comparisons will be used to statistically resolve gene expression differ-
ences 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
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