# Microarray Analysis tool

## Documentation for package ‘genArise’ version 1.16.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

a.arise | A Arise
alter.unique | Remove Duplicates
analysis.window | Analysis.window
annotations | Gene Annotations
back.gui | Return to the last window
bg.correct | Background Correction
classes | Classes Defined by this Package
create.project | create.project
cys.plot | Data Visualization: log2(Cy3) vs log2(Cy5)
DataSet-class | DataSet - class
filter.spot | Intensity-based filtering of array elements
genArise | GUI: Graphical User Interface
genArise.init | genArise.init
genMerge | genMerge: Post-Genomic Analysis
get.values | Auxiliar function for post-analysis
get.Zscore | Swap from Files
global.norm | Global Normalization of Spot
graphic.choose | Graphic choose
grid.norm | Normalization by grid of Spot
help | Help of genArise
i.arise | I Arise
imageLimma | Image Plot of Microarray
m.arise | M Arise
ma.plot | Data Visualization: M vs. A plot
make.swap | Swap analysis
meanUnique | Remove Duplicates
note | note
old.project | Open previous project
post.analysis | Set-combinatorial analysis
principal | Principal window of genAriseGUI
projects.select | File selector
r.arise | Get R value
read.dataset | Read Dataset from File
read.spot | Read Spot from File
reset.history | Reset the prj history file
ri.plot | Data Visualization: R vs I
set.grid.properties | set.grid.properties
set.history.project | Save the history of a project
set.path.project | set.path.project
set.project.properties | set.project.properties
Simon | Dataset: Little fragment of a microarray from IFC UNAM
single.norm | Swap from Files
Spot-class | Spot - class
spotUnique | Replicate filtering
swap.select | Dye swap files selector
trim | Trim
write.dataSet | Write dataSet
write.spot | Write Spot
write.zscore | Write Z-score data
WT.dataset | Microarray from the IFC
Zscore | Z-scores for identifying differential expression
Zscore.plot | Z-score Data Visualization: R vs I or M vs A
Zscore.points | Z-score Window