11 March 2014: puma 3.5.2

1. Addition of gmhta and igmoExon functions
2. Parallelization function gmhta and gmoExon and igmoExon
3. Changed the way of calculate gene and transcript values. The original calculates in R ,and now is in C

01 July 2007: puma 1.2.1

A major revision of puma. Includes the following changes:
1. Addition of a DEResults class and associated methods
2. Changed the default normalisation in mmgmos from "none" to "median"
3. Added methods for writing results to text files
4. Addition of calculateFC and calculateTtest functions
5. Addition of calcAUC and numFP functions
6. createContrastMatrix modified to additionally create "X vs other contrasts" for factors with 3 or more levels
7. removeUninformativeFactors function created to overcome problems with troublesome data sets

See SVN for more details

27 April 2007: puma 1.2.0

First version available from Bioconductor. Note this is actually the same version as 1.2.0 - I didn't quite understand the Bioconductor numbering update!

30 March 2007: puma 1.0.0

First version uploaded to Bioconductor

08 January 2007: puma 0.0.3

Version first tested with R 2.5.0

04 January 2007: puma 0.0.2

An updated version, to be used for beta testing was created.

12 October 2006: puma 0.0.1

The first version of the puma package was created, with a view to becoming part
of the Bioconductor project.

PRE-HISTORY

Parts of the puma package were originally created by Xuejun Liu as the following
separate R packages: mmgmos, pplr, pumaclust, as well as Matlab code (by Guido
Sanguinetti) for NPPCA. This legacy code is still available from the project
website http://umber.sbs.man.ac.uk/resources/puma/.
