Proceedings Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation

First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)

生物科学;医药卫生

Xiaohui Fan ; Leming Shi ; Hong Fang ; Stephen Harris ; Roger Perkins ; Weida Tong

Others  :  http://www.biomedcentral.com/content/pdf/1753-6561-3-S2-S4.pdf
PID  :  49527

来源: CEUR

【 摘 要 】

Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar studies across laboratories and platform s. The rat toxicogenomics stud y of the MicroArray Quality Control (MAQC) project empiricall y revealed that the DEGs selected using a fold change (FC)- based criterion were more reproducible than those derived solely by statistical significance such as P-value from a simple t-tests. In this study, wegenerate a set of simula ted microarray datasets to compare gene selection/ranking rules, including P-value, FC and their combinations, using the percentage of overlapping genes between DEGsfrom two similar simula ted datasets as the measure of reproducibility. The results are supportive of the MAQC's conclusion on that DEG lists are more reproducible across laboratories andplatforms when FC-based ranking coupled with a nonstringent P-value cutoff is used for gene selection compared with selection based on P-value based ranking method. We conclude that the MA QC recommendation should be considered when reproducibility is an important study objective.[First Paragraph]