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MBatch

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Overview
DescriptionR package to help assess and correct for batch effects.
Development Information
GitHub MD-Anderson-Bioinformatics/MBatch
LanguageR
LicenseGPL (>=2)
StatusActive
Help and Support
Contact Rehan Akbani 
Discussion Issues On GitHub 

MBatch

MBatch is a statistical tool that analyzes for the presence of Batch Effects in data. This tool was used to generate the data visualized in the TCGA Batch Effects website.

To download the R package:

DOWNLOAD MBATCH

To see MBatch applied to TCGA data:

LAUNCH TCGA BATCH EFFECTS WEBSITE

Help

From the R command line

help(package="MBatch")

Will list the description and the exposed functions and classes for this package.

With the package loaded, ?methodname will get the help for a method and class?classname will get the help for a class.

Cairo Prerequisites

The R Package Cairo (http://www.rforge.net/Cairo/ ) is dependent on the Cairo Graphics Library.

Please check http://www.cairographics.org/ for Windows and Linux prerequisites.

R Versions

We have compiles for Linux 64 bit R1.13.X and R1.12.X and for Windows 32 R1.13.X.

Installing Required Packages (R Command Line)

install.packages("Cairo")
install.packages("mclust")
install.packages("gtools")
install.packages("squash")
rVersion <- local(
{
   rvers <- getRversion()
   paste(rvers$maj, rvers$min, sep=".")
})
oompaRepo <- local(
{
    repoHostname <- "bioinformatics.mdanderson.org"
    oompa <- sprintf("http://%s/OOMPA/%s", repoHostname, rVersion)
    names(oompa) <- "OOMPA"
    oompa
})
install.packages(c("oompaBase", "ClassDiscovery", "PreProcess"), repos=c(getOption("repos"), oompaRepo))

Installing MBatch Windows

# <change to directory with package files>
# remove the old packages (optional)
R CMD REMOVE MBatch
# add current packages
R CMD INSTALL MBatch_*.zip

Installing MBatch Linux

# <change to directory with package files>
# remove the old packages (optional)
R CMD REMOVE MBatch
# add current packages
R CMD INSTALL MBatch_*.tar.gz

Sample Code

See MBatchSample.R file. Change the value for the baseDir variable to run on your machine.

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