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 inclusion/exclusion decision.
|Depends:||R (≥ 2.10.0), proto, foreach, iterators|
|Suggests:||doMC, doSNOW, FactoMineR, matrixStats, gdata, gtools, survival|
|Author:||Don Kang and George Tseng|
|Maintainer:||Don Kang <donkang75 at gmail.com>|
|CRAN checks:||MetaQC results|
|Windows binaries:||r-devel: MetaQC_0.1.13.zip, r-release: MetaQC_0.1.13.zip, r-oldrel: MetaQC_0.1.13.zip|
|OS X El Capitan binaries:||r-release: MetaQC_0.1.13.tgz|
|OS X Mavericks binaries:||r-oldrel: MetaQC_0.1.13.tgz|
|Old sources:||MetaQC archive|
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