Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

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Documentation for package ‘ABarray’ version 1.74.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ABarray	Utility to perform QA, data transformation and statistical analysis
ABarrayGUI	GUI for ABarray to perform QA, data transformation and statistical analysis
calcsn	Calculate SN summary for each group
concord	Calculate signal detection concordance
cvv	CV calculation
cvvPlot	Plot CV value
doANOVA	Perform one way or two way ANOVA
doLPE	Perform LPE analysis
doPlotEset	Produce a number of QA plot plus t and ANOVA test
doPlotFCT	Calculate fold change and t test, the plot
doVennDiagram	Create Venn Diagram
drawVennDiagram	Draw Venn Diagram
getMemberEset	Produce a sub ExpressionSet given a group and its members
getPantherMap	Create pie chart for probes involved in Panther Pathway
hclusterPlot	heatmap generation
icpPlot	icp plot function
imputeFlag	Perform imputation for missing values (FLAG > 5000)
lpe.fdr.BH	Perform FDR on LPE results
mamaplot	MA plot function
matrixPlot	heatmap for matrix
mvaPair2	plot MA for each pair of columns
panel.cor	Create correlation panel
panel.scatter	Creat scatter plot
qnNormalize	Perform quantile normalization
rgcolorsfunc	generate color map
savejpg	save device to jpg image file
scaleColorBar	Create scale for heatmap
snSummary	Create summary information for S/N ratio