plotWhiskers

 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

 A 2-element integer vector specifying the columns of data to be compared. 

comparisons

 The method used to sort the genes. "logRatio" is fold change. PPLR is Probability of Positive Log Ratio (as determined by the <code><a rd-options="" href="/link/pumaDE?package=puma&version=3.12.0" data-mini-rdoc="puma::pumaDE">pumaDE</a></code> method). 

sortMethod

numGenes

 The x limits of the plot. See <code><a rd-options="" href="/link/plot.default?package=puma&version=3.12.0" data-mini-rdoc="puma::plot.default">plot.default</a></code>. 

xlim

 A main title for the plot. See <code><a rd-options="" href="/link/plot.default?package=puma&version=3.12.0" data-mini-rdoc="puma::plot.default">plot.default</a></code>. 

main

 Row numbers of probesets to highlight with an asterisk. 

highlightedGenes


A plot showing error bars for genes of interest.


hplot

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)

plotWhiskers function

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

 The method used to sort the genes. "logRatio" is fold change. PPLR is Probability of Positive Log Ratio (as determined by the <code><a rd-options='' href='pumaDE'>pumaDE</a></code> method). 

 The x limits of the plot. See <code><a rd-options='' href='plot.default'>plot.default</a></code>. 

 A main title for the plot. See <code><a rd-options='' href='plot.default'>plot.default</a></code>. 

plotWhiskers: Standard errors whiskers plot

Description

Usage

Arguments

Value

See Also