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 <firstname.lastname@example.org> and George Tseng <email@example.com>|
|Date of publication||2012-12-22 07:39:42|
|Maintainer||Don Kang <firstname.lastname@example.org>|
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.