pumaDEUnsorted

 A list as output by <code><a rd-options="" href="/link/pumaDE?package=puma&version=3.12.0" data-mini-rdoc="puma::pumaDE">pumaDE</a></code>. 


Returns the output from <code><a rd-options="" href="/link/pumaDE?package=puma&version=3.12.0" data-mini-rdoc="puma::pumaDE">pumaDE</a></code> as an unsorted matrix (i.e. sorted according to the original sorting in the ExpressionSet)


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)

pumaDEUnsorted function

 A list as output by <code><a rd-options='' href='pumaDE'>pumaDE</a></code>. 


Returns the output from <code><a rd-options='' href='pumaDE'>pumaDE</a></code> as an unsorted matrix (i.e. sorted according to the original sorting in the ExpressionSet)


pumaDEUnsorted: Return an unsorted matrix of PPLR values

Description

Usage

Arguments

Value

See Also