Image Analysis and Data Normalization Procedures are Crucial for Microarray Analyses

Abstract: This study was conducted with the aim of optimizing the experimental design of array experiments. We compared two image analysis and normalization procedures prior to data analysis using two experimental designs. For this, RNA samples from Charolais steers Longissimus thoracis muscle and subcutaneous adipose tissues were labeled and hybridized to a bovine 8,400 oligochip either in triplicate or in a dye-swap design. Image analysis and normalization were processed by either GenePix/MadScan or ImaGene/GeneSight. Statistical data analysis was then run using either the SAM method or a Student’s t-test using a multiple test correction run on R 2.1 software. Our results show that image analysis and normaliza-tion procedure had an impact whereas the statistical methods much less infl uenced the outcome of differentially expressed genes. Image analysis and data normalization are thus an important aspect of microarray experiments, having a potentially signifi cant impact on downstream analyses such as the identifi cation of differentially expressed genes. This study provide