numOfFactorsToUse

 An object of class
	  <code><a rd-options="Biobase:class.ExpressionSet" href="/link/ExpressionSet?package=puma&version=3.12.0&to=Biobase%3Aclass.ExpressionSet" data-mini-rdoc="Biobase:class.ExpressionSet::ExpressionSet">ExpressionSet</a></code>. 

eset


This is really an internal function used to determine how many factors to use in design and contrast matrices

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)

numOfFactorsToUse function

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

numOfFactorsToUse: Determine number of factors to use from an ExpressionSet

Description

Usage

Arguments

Value

See Also

Examples