pumaPCAExpectations-class

pumaPCAExpectations


This is a class representation for storing a set of expectations from a pumaPCA model. It is an internal representation and shouldn't normally be instantiated.


classes

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)

pumaPCAExpectations-class function

Objects can be created by calls of the form <code>new("pumaPCAExpectations", ...)</code>.

Objects from the Class

<dl>
		<dt><code>x</code>:</dt><dd>Object of class "matrix" representing x</dd> <dt><code>xxT</code>:</dt><dd>Object of class "array" representing xxT</dd> <dt><code>logDetCov</code>:</dt><dd>Object of class "numeric" representing logDetCov</dd> </dl> 

Slots

Methods

This is a class representation for storing a set of expectations from a pumaPCA model. It is an internal representation and shouldn't normally be instantiated.

pumaPCAExpectations-class: Class pumaPCAExpectations

Description

Arguments

Objects from the Class

Slots

Methods

See Also