normalisation.gs

 a matrix or data frame which contains gene expression level on log2 scale. 

This function is only included for backwards compatibility with the pplr package. This function is now superceded by <code><a rd-options="" href="/link/pumaNormalize?package=puma&version=3.14.0" data-mini-rdoc="puma::pumaNormalize">pumaNormalize</a></code>.This function does the global scaling normalisation.

 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)

normalisation.gs function

a matrix or data frame which contains gene expression level on log2 scale.

This function is only included for backwards compatibility with the <pkg>pplr</pkg> package. This function is now superceded by <code><a href="pumaNormalize" rd-options="">pumaNormalize</a></code>.

This function does the global scaling normalisation.

normalisation.gs: Global scaling normalisation

Description

Usage

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Details

See Also

Examples