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AMEN Changelog

What's new in AMEN 1.5.0

Nov 20, 2012
  • Changes:
  • The most important changes since 2006: Annotation and Network data files are now automatically generated!
  • There's no more need to download different databases and convert them! Just use the "Menu>Options>Download databases" module.
  • "Main entries" are now called "Reference entries".
  • Annotation and interaction data files could now include "multi-reference entries" (separated by semi-colon ';') as "reference entries" (1rst column)
  • "Upload data" was removed and associated modules were placed into either "Expression" or "Options" menu
  • Modules:
  • Two modules allowing one to make the union/intersection of several groups (>=2).
  • Bugs fixed:
  • Bugs in the "Network drawing" and "Community structure detection" modules due to changes in the "igraph" package.

New in AMEN 1.3.4 (Mar 9, 2011)

  • Impossible to add gene2go information to an annotation file from IPI.
  • Impossible to run some normalization modules and especially the "Surface Intensity Distribution".

New in AMEN 1.3.3 (Oct 18, 2010)

  • Two changes:
  • Network drawing module has changed
  • Complete "Annotation file with gene2go" module has changed. Now, the previous annotation is replaced by the gene2go annotations.
  • Two bugs fixed:
  • The "partial correlation network" output file was incomplete.
  • Problem with some generated Expression data files containing a empty character at the first position of the header (first line).

New in AMEN 1.3.2 (Sep 13, 2010)

  • One module:
  • A Community Structure Detection (CSD) module (based on the igrpah R library) was
  • added into AMEN in order to detect motifs on network.
  • One change:
  • Less (memory) restrictions when loading huge "statistics" data file.
  • One minor bug fixed:
  • Problems during the conversion of the NCBI proteome file.

New in AMEN 1.3.1 (Jul 27, 2010)

  • One minor bug fixed:
  • Impossible to run a "Quantile-quantile normalization" properly.

New in AMEN 1.2.9 (Jul 20, 2010)

  • One major change:
  • The GraphViz program is now replace by the "igraph" R library. So now, no need to
  • install GraphViz prior to execute AMEN.
  • One minor change:
  • The "interaction" panel into the AMEN GUI was renamed by "network".
  • 4 modules:
  • A module allowing one to automatically import protein-protein and protein-gene
  • association data available at the TFe (Transcription Factor encyclopedia) was added.
  • A module dedicated to partial correlation network analysis (using the "GeneNet"
  • R library) was added.
  • A module dedicated to detection of periodically expressed genes (using the "GeneCycle"
  • R library) was added.
  • A module dedicated to "InterQuartile Range Filtration" was added.
  • One minor bug fixed:
  • Incompatibility with Windows 7 during the first AMEN execution when the program
  • tried to find automatically the R binary file.

New in AMEN 1.2.8 (Apr 19, 2010)

  • Two modules:
  • A module is available to import the NCBI 'interactions' data file
  • A module is available to import the NIA MPPI data file
  • Changes:
  • AMEN is now able to import interaction data from DIP, HPRD, CORUM, MatrixDB
  • "protein-ribonculeic acid" interactions were renamed "protein-rna" interactions

New in AMEN 1.2.7 (Apr 6, 2010)

  • bug into the AMEN Graphical User Interface.

New in AMEN 1.2.6 (Apr 1, 2010)

  • Brand new AMEN Graphicla User Interface
  • No more restrictions on the length names
  • Synonyms and ORFNames are now extracted when converting EBI proteome file (.dat)

New in AMEN 1.2.5 (Mar 31, 2010)

  • Two changes:
  • A module is now available to pre-process the Affymetrix Exon Array as
  • well as Affymetrix Gene Array CEL files. Users should download the CDF file available
  • for each microarray in the "library files" section (into the support menu)
  • A module is now available to import the Affymetrix Exon Array as
  • well as Affymetrix Gene Annotation files (CSV files). Users should download the CSV file available
  • for each microarray in the "annotation data" section (into the support menu)
  • Four bugs fixed:
  • Redundancies in the "Group" column when exporting data as HTML table. It happened if there were redundancies in
  • the group files.
  • Impossible to convert the BioGRID interaction PSIMI-2.5 files due to changes in their format.
  • Impossible to extract the participant identification methods from the MINT and BioGRID interaction
  • PSIMI-2.5 files.
  • An unnecessary message was displayed if the IMG package was not installed. PNG format is now automatically supported by Tcl/Tk 8.6

New in AMEN 1.2.4 (Mar 25, 2010)

  • AMEN was enable to install the required R packages if the path to AMEN contained space characters.

New in AMEN 1.2.3 (Mar 20, 2010)

  • change:
  • The missing files (deleted or moved or renamed) in the project will not be loaded into the AMEN interface.
  • minor bugs fixed:
  • Impossible to display KEGG pathways anymore.
  • Impossible to select a pathway indicated into the displayed KEGG pathway. This bug is due to a change into the KEGG web site.

New in AMEN 1.2.2 (Mar 19, 2010)

  • A Quality-control module after normalization is now available for intensity signal data directly added to the 'Expression' panel. This module includes boxplot, scatterplot and correlation matrix pictures saved into pdf files.
  • A log2-/unlog2-transformation module was added.
  • A new visualization module allows user to display the expression signals using a radar view.

New in AMEN 1.1.7 (Jun 4, 2009)

  • 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.

New in AMEN 1.1.5 (Nov 14, 2008)

  • Bug fixes:
  • A problem when indexing expression data file (ExpressionPanel procedure) gave several problems in procedure using these expression data files and especially statistical modules (Standard deviation, Find similar patterns, Limma modules). These errors occured when not all the samples were selected.
  • Changes:
  • Over/under-representation module allows one to estimate enrichment by comparing groups together and not only by comparing groups to whole genome.
  • Affymetrix All-exon modules use now the "transcript cluster ids" to estimate the Gene-level intensity signals.
  • KEGG importation module ask the user to select the interesting species for his current project.
  • KEGG visualization module allows users to choose between several species for the same pathway.