Package: ABarray 1.79.0

Yongming Andrew Sun

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

Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

Authors:Yongming Andrew Sun

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ABarray.pdf |ABarray.html✨
ABarray/json (API)

# Install 'ABarray' in R:

install.packages('ABarray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ABarray-1.79.0(bioc 3.23)ABarray-1.78.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray onechannel preprocessing

4.20 score 3 scripts 466 downloads 4 mentions 28 exports 8 dependencies

Last updated from:839d701559. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Total time
bioc-checks	ERROR	150
linux-devel-x86_64	NOTE	137
source / vignettes	OK	196
linux-release-x86_64	NOTE	131
macos-release-arm64	NOTE	155
macos-oldrel-arm64	NOTE	91
windows-devel	NOTE	92
windows-release	NOTE	93
windows-oldrel	NOTE	99
wasm-release	OK	93

Exports:ABarray ABarrayGUI calcsn concord cvv cvvPlot doANOVA doLPE doPlotEset doPlotFCT doVennDiagram drawVennDiagram getMemberEset getPantherMap hclusterPlot icpPlot imputeFlag lpe.fdr.BH mamaplot matrixPlot mvaPair2 panel.cor panel.scatter qnNormalize rgcolorsfunc savejpg scaleColorBar snSummary

Dependencies:Biobase BiocGenerics generics lattice MASS Matrix multtest survival

ABarray gene expression

Rendered fromABarray.Rnwusingutils::Sweaveon Dec 11 2025.

Last update: 2013-11-01
Started: 2013-11-01

ABarray gene expression GUI interface

Rendered fromABarrayGUI.Rnwusingutils::Sweaveon Dec 11 2025.

Last update: 2013-11-01
Started: 2013-11-01

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

Package: ABarray 1.79.0

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

ABarray gene expression

ABarray gene expression GUI interface

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Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)