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.

Author
Yongming Andrew Sun
Date of publication
None
Maintainer
Yongming Andrew Sun <sunya@appliedbiosystems.com>
License
GPL
Version
1.42.0

View on Bioconductor

Man pages

ABarray
Utility to perform QA, data transformation and statistical...
ABarrayGUI
GUI for ABarray to perform QA, data transformation and...
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

Files in this package

ABarray/DESCRIPTION
ABarray/NAMESPACE
ABarray/R
ABarray/R/ABarray.R
ABarray/R/ABarrayGUI.R
ABarray/R/attachMessage.R
ABarray/R/calcsn.R
ABarray/R/concord.R
ABarray/R/cvv.R
ABarray/R/cvvPlot.R
ABarray/R/doANOVA.R
ABarray/R/doLPE.R
ABarray/R/doPlotEset.R
ABarray/R/doPlotFCT.R
ABarray/R/doVennDiagram.R
ABarray/R/drawVennDiagram.R
ABarray/R/getMemberEset.R
ABarray/R/getPantherMap.R
ABarray/R/hclusterPlot.R
ABarray/R/icpPlot.R
ABarray/R/imputeFlag.R
ABarray/R/lpe.fdr.BH.R
ABarray/R/mamaplot.R
ABarray/R/matrixPlot.R
ABarray/R/mvaPair2.R
ABarray/R/panel.cor.R
ABarray/R/panel.scatter.R
ABarray/R/qnNormalize.R
ABarray/R/rgcolorsfunc.R
ABarray/R/savejpg.R
ABarray/R/scaleColorBar.R
ABarray/R/snSummary.R
ABarray/build
ABarray/build/vignette.rds
ABarray/inst
ABarray/inst/doc
ABarray/inst/doc/ABarray.Rnw
ABarray/inst/doc/ABarray.pdf
ABarray/inst/doc/ABarrayGUI.Rnw
ABarray/inst/doc/ABarrayGUI.pdf
ABarray/man
ABarray/man/ABarray.Rd
ABarray/man/ABarrayGUI.Rd
ABarray/man/calcsn.Rd
ABarray/man/concord.Rd
ABarray/man/cvv.Rd
ABarray/man/cvvPlot.Rd
ABarray/man/doANOVA.Rd
ABarray/man/doLPE.Rd
ABarray/man/doPlotEset.Rd
ABarray/man/doPlotFCT.Rd
ABarray/man/doVennDiagram.Rd
ABarray/man/drawVennDiagram.Rd
ABarray/man/getMemberEset.Rd
ABarray/man/getPantherMap.Rd
ABarray/man/hclusterPlot.Rd
ABarray/man/icpPlot.Rd
ABarray/man/imputeFlag.Rd
ABarray/man/lpe.fdr.BH.Rd
ABarray/man/mamaplot.Rd
ABarray/man/matrixPlot.Rd
ABarray/man/mvaPair2.Rd
ABarray/man/panel.cor.Rd
ABarray/man/panel.scatter.Rd
ABarray/man/qnNormalize.Rd
ABarray/man/rgcolorsfunc.Rd
ABarray/man/savejpg.Rd
ABarray/man/scaleColorBar.Rd
ABarray/man/snSummary.Rd
ABarray/vignettes
ABarray/vignettes/ABarray.Rnw
ABarray/vignettes/ABarrayGUI.Rnw
ABarray/vignettes/Figure
ABarray/vignettes/Figure/ab1700gui.pdf
ABarray/vignettes/Figure/dirChangeFig.pdf
ABarray/vignettes/Figure/dirSelectFig.pdf
ABarray/vignettes/Figure/venn-threeWay.pdf
ABarray/vignettes/Figure/venn-twoWay.pdf