To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("blima")

In most cases, you don't need to download the package archive at all.

blima

 

This is the development version of blima; for the stable release version, see blima.

Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.

Bioconductor version: Development (3.3)

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

Author: Vojtech Kulvait

Maintainer: Vojtech Kulvait <kulvait at gmail.com>

Citation (from within R, enter citation("blima")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("blima")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("blima")

 

PDF blima.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Microarray, Normalization, Preprocessing, Software
Version 1.5.0
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 3.0.0)
Imports beadarray(>= 2.0.0), Biobase(>= 2.0.0), BiocGenerics, grDevices, stats, graphics
LinkingTo
Suggests xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi
SystemRequirements
Enhances
URL https://bitbucket.org/kulvait/blima
Depends On Me
Imports Me
Suggests Me blimaTestingData
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source blima_1.5.0.tar.gz
Windows Binary blima_1.5.0.zip
Mac OS X 10.6 (Snow Leopard) blima_1.3.0.tgz
Mac OS X 10.9 (Mavericks) blima_1.5.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/blima
Package Short Url http://bioconductor.org/packages/blima/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center