requireAll

A character vector of required packages. Unavailable packages are going to be installed.

packages

require

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.

requireAll: MetaQC: Quantitative Quality Assessment for Inclusion/Exclusion Criteria of Genomic Meta-Analysis

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