exampleE


  This data is an artificial example of the mean gene expression levels from 
  golden spike-in data set in Choe et al. (2005).


datasets

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)

exampleE function

A 200x6 matrix including 200 genes and 6 chips. The first 3 chips are replicates for 
  C condition and the last 3 chips are replicates for S conditon.

Format

Choe,S.E., Boutros,M., Michelson,A.M., Church,G.M., Halfon,M.S.: 
  Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. 
  Genome Biology, 6 (2005) R16.

exampleE: The example data of the mean gene expression levels

Description

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See Also