calculateTtest

 An object of class <code><a rd-options="Biobase:class.ExpressionSet" href="/link/ExpressionSet?package=puma&version=3.14.0&to=Biobase%3Aclass.ExpressionSet" data-mini-rdoc="Biobase:class.ExpressionSet::ExpressionSet">ExpressionSet</a></code> 

eset

design.matrix

contrast.matrix


Automatically creates design and contrast matrices if not specified. This function is useful for comparing T-test results with those of other differential expression (DE) methods such as <code><a rd-options="" href="/link/pumaDE?package=puma&version=3.14.0" data-mini-rdoc="puma::pumaDE">pumaDE</a></code>.


manip

Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Xuejun Liu

puma

Propagating Uncertainty in Microarray Analysis(including
Affymetrix tranditional 3' arrays and exon arrays and Human
Transcriptome Array 2.0)

calculateTtest function

An object of class <code><a href="ExpressionSet" rd-options="Biobase:class.ExpressionSet">ExpressionSet</a></code>

Automatically creates design and contrast matrices if not specified. This function is useful for comparing T-test results with those of other differential expression (DE) methods such as <code><a href="pumaDE" rd-options="">pumaDE</a></code>.

calculateTtest: Calculate differential expression between conditions using T-test

Description

Usage

Arguments

Value

Details

See Also

Examples