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

## Documentation for package ‘iCheck’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
sortExpressionSet | Sort the order of samples for an ExpressionSet object