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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
1.0.0
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Version
1.2.0
License
GPL (>= 2)
Maintainer
Weiliang Qiu
Last Published
September 29th, 2015
Functions in iCheck (1.2.0)
Search functions
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