MetaQC: 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 inclusion/exclusion decision.

Version: 0.1.13
Depends: R (≥ 2.10.0), proto, foreach, iterators
Suggests: doMC, doSNOW, FactoMineR, matrixStats, gdata, gtools, survival
Published: 2012-12-22
Author: Don Kang and George Tseng
Maintainer: Don Kang <donkang75 at gmail.com>
License: GPL-2
URL: https://github.com/donkang75/MetaQC
NeedsCompilation: no
In views: MetaAnalysis
CRAN checks: MetaQC results

Downloads:

Reference manual: MetaQC.pdf
Package source: MetaQC_0.1.13.tar.gz
OS X binary: MetaQC_0.1.13.tgz
Windows binary: MetaQC_0.1.13.zip
Old sources: MetaQC archive