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iCheck (version 1.2.0)

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

Description

QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

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Version

Version

1.2.0

License

GPL (>= 2)

Maintainer

Weiliang Qiu

Last Published

February 15th, 2017

Functions in iCheck (1.2.0)

getPCAFunc

Get principal components of arrays
pca3DPlot

Scatter plot of 3 specified principal components
plotSamplep95p05

Plot trajectories of the ratio of 95th percentile to 5th percentile of sample probe profiles across arrays
sortExpressionSet

Sort the order of samples for an ExpressionSet object
quantilePlot

Plot trajectories of quantiles across arrays
plotQCCurves

Plot trajectories of specific QC probes (e.g., biotin, cy3_hyb, housekeeping gene probes, low stringency probes, etc.) across arrays
plotCurves

Plot trajectories of probe profiles across arrays
genSimData.BayesNormal

Generating simulated data set from conditional normal distributions
glmWrapper

Perform glm test for all gene probes
lmFitPaired

A wrapper function for the function 'lmFit' of the R Bioconductor package 'limma' for paired data
LumiBatch2Table

Output slots (exprs, pData, fData) of an LumiBatch object into 3 text files
pca2DPlot

Scatter plot of first 2 principal components
lmFitWrapper

A wrapper function for the function 'lmFit' of the R Bioconductor package 'limma'
genExprSet

Generate an ExpressionSet object
R2PlotFunc

Draw heatmap of square of correlations among arrays
lkhrWrapper

Perform glm test for all gene probes