QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Documentation for package ‘iCheck’ version 1.20.0

boxPlots	Draw parallel plots for top results in whole-genome-wide analysis
densityPlots	Draw estimated density plots for all arrays
genExprSet	Generate an ExpressionSet object
genSimData.BayesNormal	Generating simulated data set from conditional normal distributions
getPCAFunc	Get principal components of arrays
glmWrapper	Perform glm test for all gene probes
lkhrWrapper	Perform glm test for all gene probes
lmFitPaired	A wrapper function for the function 'lmFit' of the R Bioconductor package 'limma' for paired data
lmFitWrapper	A wrapper function for the function 'lmFit' of the R Bioconductor package 'limma'
LumiBatch2Table	Output slots (exprs, pData, fData) of an LumiBatch object into 3 text files
pca2DPlot	Scatter plot of first 2 principal components
pca3DPlot	Scatter plot of 3 specified principal components
plotCurves	Plot trajectories of probe profiles across arrays
plotQCCurves	Plot trajectories of specific QC probes (e.g., biotin, cy3_hyb, housekeeping gene probes, low stringency probes, etc.) across arrays
plotSamplep95p05	Plot trajectories of the ratio of 95th percentile to 5th percentile of sample probe profiles across arrays
quantilePlot	Plot trajectories of quantiles across arrays
R2PlotFunc	Draw heatmap of square of correlations among arrays
scatterPlots	Draw scatter plots for top results in whole-genome-wide analysis
sortExpressionSet	Sort the order of samples for an ExpressionSet object