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

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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.

Author
Don Kang <donkang75@gmail.com> and George Tseng <ctseng@pitt.edu>
Date of publication
2012-12-22 07:39:42
Maintainer
Don Kang <donkang75@gmail.com>
License
GPL-2
Version
0.1.13
URLs

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Man pages

brain
7 brain cancer studies
cleanup
Cleaning up resources.
MetaQC
MetaQC: Objective Quality Control and Inclusion/Exclusion...
MetaQC-package
MetaQC: Objective Quality Control and Inclusion/Exclusion...
plot.proto
Plot MetaQC results.
print.proto
Print MetaQC results.
requireAll
MetaQC: Quantitative Quality Assessment for...
runQC
Command to execute quality control procedures.

Files in this package

MetaQC
MetaQC/MD5
MetaQC/R
MetaQC/R/runQC.R
MetaQC/R/requireAll.R
MetaQC/R/MetaQC.R
MetaQC/R/functions.R
MetaQC/R/cleanup.R
MetaQC/NAMESPACE
MetaQC/man
MetaQC/man/runQC.Rd
MetaQC/man/requireAll.Rd
MetaQC/man/print.proto.Rd
MetaQC/man/plot.proto.Rd
MetaQC/man/MetaQC.Rd
MetaQC/man/MetaQC-package.Rd
MetaQC/man/cleanup.Rd
MetaQC/man/brain.Rd
MetaQC/DESCRIPTION
MetaQC/data
MetaQC/data/datalist
MetaQC/data/brain.rda