Learn R Programming

ABarray (version 1.40.0)

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

Description

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.

Copy Link

Version

Version

1.40.0

License

GPL

Maintainer

Yongming Andrew Sun

Last Published

February 15th, 2017

Functions in ABarray (1.40.0)

ABarrayGUI

GUI for ABarray to perform QA, data transformation and statistical analysis
ABarray

Utility to perform QA, data transformation and statistical analysis
mamaplot

MA plot function
matrixPlot

heatmap for matrix
rgcolorsfunc

generate color map
savejpg

save device to jpg image file
doPlotEset

Produce a number of QA plot plus t and ANOVA test
calcsn

Calculate SN summary for each group
concord

Calculate signal detection concordance
doVennDiagram

Create Venn Diagram
drawVennDiagram

Draw Venn Diagram
mvaPair2

plot MA for each pair of columns
icpPlot

icp plot function
hclusterPlot

heatmap generation
qnNormalize

Perform quantile normalization
panel.scatter

Creat scatter plot
doPlotFCT

Calculate fold change and t test, the plot
getMemberEset

Produce a sub ExpressionSet given a group and its members
getPantherMap

Create pie chart for probes involved in Panther Pathway
panel.cor

Create correlation panel
doANOVA

Perform one way or two way ANOVA
doLPE

Perform LPE analysis
scaleColorBar

Create scale for heatmap
snSummary

Create summary information for S/N ratio
cvv

CV calculation
cvvPlot

Plot CV value
imputeFlag

Perform imputation for missing values (FLAG > 5000)
lpe.fdr.BH

Perform FDR on LPE results