MetaQC (0.1.13)

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MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis.

https://github.com/donkang75/MetaQC
http://cran.r-project.org/web/packages/MetaQC

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.

Maintainer: Don Kang
Author(s): Don Kang <donkang75@gmail.com> and George Tseng <ctseng@pitt.edu>

License: GPL-2

Uses: foreach, iterators, proto, FactoMineR, gdata, gtools, survival, matrixStats, doMC, doSNOW

Released almost 7 years ago.

10 previous versions

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