AMEN

File Release Notes and Changelog

Release Name: 1.1.7

Notes:
VERSION:1.1.7
- Four bugs fixed!

The AMEN_Windows_1.1.7.exe Windows 32-bit binary file automatically installs (user must have the administrative privileges) : ActiveTcl version 8.5.2.0 ; R version 2.7.1 ; GraphViz version 2.17. IMPORTANTLY, once AMEN has been successfully installed, user must directly "Launch AMEN" from the installation process to install the three integrated programs!

IMPORTANT: You must directly "Launch AMEN" at the end of this installation process" to correctly install the R, ActiveTcl and GraphViz programs!!!
IMPORTANT: If users have the administrative privileges, AMEN will automatically install required R packages. If not, users must manually install the following R packages: Biobase, splines, tools, affyio, affy, matchprobes, gcrma, lumi, annotate, mgcv, limma, cluster, survival, multtest, mclust, hopach, RankProducts, samr, gtools, clValid, kohonen, dynamicTreeCut
These libraries can be downloaded at
http://cran.ch.r-project.org
http://www.bioconductor.org/packages/bioc


Changes:
Three bugs occured when expression data contained missing values in the following modules:
- Average/median expression calculation
- Standard deviation filtration
- Standardized normalization

The "affy" package does not provide the "normalize.quantiles" function anymore. AMEN now uses the "normalizeBetweenArrays" function from the "Limma" package into the quantile-quantile normalization module.