Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data

Background: Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms. The MAQC analysis presented for the conclusion of inter- and intra-platform comparability/ reproducibility of microarray gene expression measurements is inadequate. We evaluate the reproducibility/comparability of the MAQC data for 12901 common genes in four titration samples generated from five high-density one-color microarray platforms and the TaqMan technology. We discuss some of the problems with the use of correlation coefficient as metric to evaluate the inter- and intraplatform reproducibility and the percent of overlapping genes (POG) as a measure for evaluation of a gene selection procedure by MAQC. Results: A total of 293 arrays were used in the intra- and inter-platf...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: James J. Chen, Huey-miin Hsueh, Robert R. Delongchamp, Chien-Ju Lin, Chen-An Tsai
• Keywords: BMCBI 2007, Gene Expression Data, Microarray Gene Expression, Overlapping Gene