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

## Documentation for package ‘ABarray’ version 1.42.0

- 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