********************
Changes in EMA1.3.1
********************

- clust.dist.R
Changes in correlation function

- plotSample.R
Add ellipses in the graphical output

- clustering.plot.R
Bug in heatmap legend
Stopifnot colnames data

- km
Graphical options changed


- clustering.plot.R
lab and lab.sup can be data.frame, casting to matrix is done manually
new option legend.pos allows the user to choose the legend position

- genes.selection
the user can specify the quantile to be computed to filter the genes



********************
Changes in EMA1.2
********************

- Add NAMESPACE file and update DESCRIPTION file

- Hide the following internals functions :
clust.dist, dice, FWER.Bonf, goReport, GSA.correlate.txt, htmlresult, jaccard, keggReport, MFAreport, qualitySample

- Remove the following functions :
plotExplore.R, mult.clustering.R

- runGSA.R
Add gene scores in output

- runInTest.R
Update of the plot in output

- runHyperGO
Bug ifnotfound mget function

- runHyperKEGG
Bug ifnotfound mget function

- normAffy
Bug missing function

- vignette updated

********************
Changes in EMA1.1
********************

- runPCA.R
* Bug : plotVariable option.
* Label is not initialized.

- clustering.plot.R
* A legend is added when a label is specified
* If data is specified, an heatmap is displayed in one way clustering
* The margins were adjusted according to the names length
* Deals with NA values in labels

- bioMartAnnot.R
* Bug : outputTypeId undefined

- probePlots.R
* Bug : cex.axis option
* Add a legend

- distrib.plot.R
* Change display using density plot instead of histogram

- sample.plot.R
* Legend is displayed out of the graph

- eval.stability.clustering.R
* Details section is added in the man page

- test.LC.R
* Global parameter : if someone want to perform a F test of the global hypothesis H_0=0, or to test each contrast simultaneously
* Add multiple testing correction

- FDR-BH.R
* Bug in the Two-stages procedure. The error rate parameter (q) is missing.

- runMFA.R
* Can write a pdf report or a txt report

- runHyperGO
* CategorySize is used to generate all the report

- man pages updated
- vignette updated
