blima (version 1.6.0)

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

Description

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.

Details

Package:

blima

Type:

Package

Title:

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

Version:

1.1.03

Date:

2015-04-01

Author:

Vojtech Kulvait

Maintainer:

Vojtech Kulvait

License:

GPL-3

LazyLoad:

yes

Depends:

R(>= 3.0.0)

Imports:

beadarray(>= 2.0.0), Biobase(>= 2.0.0), BiocGenerics, grDevices, stats, graphics

Suggests:

xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi

URL:

https://bitbucket.org/kulvait/blima

biocViews:

Microarray, Preprocessing, Normalization