MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis MetaQC implements our proposed quantitative quality control measures: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). (See the reference for detailed explanation.) For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclustion/exclusion decision. Software Depends: R (>= 2.10.0), proto, foreach, iterators Suggests: doMC, doSNOW, FactoMineR, matrixStats, gdata, gtools, survival Don Kang <donkang75@gmail.com> Don Kang <donkang75@gmail.com> and George Tseng <ctseng@pitt.edu> GPL-2 2012-04-27 application/tgz http://CRAN.R-project.org/package=MetaQC