Schematic process diagram of M2DB. Affymetrix GeneChip HG-U133A and HG-U133 Plus 2.0 arrays with CEL files are downloaded from GEO and ArrayExpress. Then, raw data was pre-processed using MAS5, RMA, and GCRMA. All arrays were annotated into five annotations via manual curation. Array quality assessed by SimpleAffy, PMVO, and MDQC packages in Bioconductor. MAS5call and labeling efficiency values (LEVs) are supplied for gene-based filtering for further analysis. Finally, all information was stored in M2DB.