Package: MetaQC
Type: Package
Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Version: 0.1.5
Author: Don Kang <donkang75@gmail.com> and George Tseng
<ctseng@pitt.edu>
Maintainer: Don Kang <donkang75@gmail.com>
Description: 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 inclustion/exclusion decision.
Depends: R (>= 2.10.0), proto, foreach
Suggests: doMC, doSMP, FactoMineR, samr, matrixStats, gdata, gtools
License: GPL-2
URL: https://github.com/donkang75/MetaQC
LazyLoad: yes
Collate: MetaQC.R requireAll.R functions.R runQC.R cleanup.R
Date: 2011-06-15
Packaged: 2011-06-15 16:26:15 UTC; don
Repository: CRAN
Date/Publication: 2011-06-15 18:49:58

Package: MetaQC
Type: Package
Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Version: 0.1.6
Author: Don Kang <donkang75@gmail.com> and George Tseng
<ctseng@pitt.edu>
Maintainer: Don Kang <donkang75@gmail.com>
Description: 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 inclustion/exclusion decision.
Depends: R (>= 2.10.0), proto, foreach
Suggests: doMC, doSMP, FactoMineR, samr, matrixStats, gdata, gtools
License: GPL-2
URL: https://github.com/donkang75/MetaQC
LazyLoad: yes
Collate: MetaQC.R requireAll.R functions.R runQC.R cleanup.R
Date: 2011-10-17
Packaged: 2011-10-17 19:08:40 UTC; don
Repository: CRAN
Date/Publication: 2011-10-18 05:59:12