Performance comparison of Affymetrix and Illumina microarray technologies_AffymetrixDataset

The present study was conducted to compare the ability of Affymetrix and Illumina microarray technologies to characterize the differential gene expression profiles of human monocytes and monocyte-derived-macrophages. Keywords: Type Cross-platform comparison Summary Blood samples were obtained from patients with symptoms of acute coronary syndrome who had undergone coronary angiography at the department of cardiology of the Pitié-Salpêtrière Hospital, Paris and who had one stenosis >50 % diagnosed in at least one major coronary artery. RNA samples were extracted from monocyte and monocyte derived macrophage cells. Five biological replicates for each type of sample were hybridized in parallel to the Affymetrix HGU133 plus 2.0 and Illumina Bead Chip Human-6 v1 platforms. In addition, a reference list of differentially expressed genes was generated from a larger number of hybridizations (mRNA from 86 individuals) using a third technology (the academic RNG/MRC two-color chip) and was used as reference to assess the performance of the 2 platforms based on 10 samples. The internal consistency of each platform, the overlap in lists of genes identified as differentially expressed generated on each array type and the biological relevance of significant genes identified on each platform (Gene Ontology (GO) classes enrichments) were assessed.