Abstract
Several species of bacteria are involved in the production of cheese, including Lactobacillus brevis and Lactococcus lactis. A custom-designed Affymetrix microarray was recently developed to study gene expression in three organisms on a single chip. This array contains only perfect match features for the coding and non-coding regions in the genomes of all three sequences. The multi-species nature of this array version raises interesting questions regarding the preprocessing or normalization strategies for the analysis of gene expression data. We present and evaluate several possible strategies using both cDNA dilution data and experimental expression data from a repeated measures design. The statistical protocols highlighted in this work are applicable to other multi-species microarrays.
Keywords
microarray, normalization, multi-species, preprocessing
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Recommended Citation
Stevens, John R.; Ganesan, Balasubramanian; Desai, Prerak; Rajan, Sweta; and Weimer, Bart C.
(2008).
"STATISTICAL ISSUES IN THE NORMALIZATIONOF MULTI-SPECIES MICROARRAY DATA,"
Conference on Applied Statistics in Agriculture.
https://doi.org/10.4148/2475-7772.1096
STATISTICAL ISSUES IN THE NORMALIZATIONOF MULTI-SPECIES MICROARRAY DATA
Several species of bacteria are involved in the production of cheese, including Lactobacillus brevis and Lactococcus lactis. A custom-designed Affymetrix microarray was recently developed to study gene expression in three organisms on a single chip. This array contains only perfect match features for the coding and non-coding regions in the genomes of all three sequences. The multi-species nature of this array version raises interesting questions regarding the preprocessing or normalization strategies for the analysis of gene expression data. We present and evaluate several possible strategies using both cDNA dilution data and experimental expression data from a repeated measures design. The statistical protocols highlighted in this work are applicable to other multi-species microarrays.
