Expander version 6 includes the follwoing improvements: =========================================================== 1)Addition of Degas tool for network-based clustering 2)Addition of ISA algorithm for bi-clustering 3)Addition of an option to extract groups from hierarchical clustering (either by manual selection or according to tree node distance) 4)Support for similarity data (i.e. similarity dmatrix can be loaded as the main data file and clustered using hierarchcal clustering) 5)Added a "Differential expression filter results" view to the data view after applying SAM/t-test as filter methods. This tab contains the p/qvalues as well as fold-change information 6)Reduced waiting time for opening a single cluster view inside a clustering results visualization 7)Improved (significantly reduced) k-means runing time 8) Changed main menu so that all actions previously activated by "Export to text" items along with "Save Solution" items can now be operated from one item (File>>Export to text) 9) Remove the "Import file" option from the Load cel files dialod box. This option used to utilize the Aroma affymetrix package, and required temp directories to be generated by Expander. However, not all OSs support this and thus cause the entire operation to fail. The analysis can be performed by downloading cdf package from Bioconductor and using the "Use R package" option. Version 6.01 additions ========================== 1) Fixed bug that prevented loading ver 5.2 sessions to ver 6. 2) Fixed bug that prevented right side panel from appearing when selecting a cluster or bi-cluster from a grouping display. 3) Fixed bug that prevented loading biclustering solutions that contained spaces in probe or condition IDs. Addition from 25/1 ====================== Added image to compbioLib that prevented from opening a similarity view Version 6.02 additions ========================== 1) Fixed bug that caused scale missmatch when zooming in on a hierarchical clustering solution. 2) Added missing organism name after preprocessing cel files 3) Expanded probe merge functionality to allow selection between several operation modes 4) Fixed bug causing a crash when the user attempts to generate a clustering solution from exported subtrees and none were exported. Version 6.03 additions ========================== Fixed bug causing Expander to fail in displaying Matisse single module view (Only replaced compbioLib.jar) Version 6.04 additions ========================== 1) Ability to open Kegg maps on the web from a KEGG enrichment analysis results (relevant genes are highlighted on map) 2) Scatter plot menu items were moved to Visualization menu. 3) Default background set was changed to "original data" in all enrichment analysis 4) ".zip" restriction was removed from session file name (is now automatically added 5) Similarity threshold input field was added to similarity clustering 6) Reference probe selection combo of similarity clustering was set to editable and the ID can now be typed instead of selected 7) Correction to SAM bug that caused errors in results 8) Added ability to load conversion file when loading gene groups 9) Corrected analysis wizard to better handle cases of missing organism data (grouping analysis dialog is not displayed) Version 6.04_1 additions ========================== Correction to a bug that caused problems in saving and loading sessions with java7 (Updated XStream package and changed manifes accordingly) Version 6.05 additions ========================== 1) Correction of a t-test bug that caused some of the differentially expressred genes to be missed 2) Correction of bug in loadin sessions using version 6.04_1 Version 6.05_1 additions ========================== Corrected a bug that caused t-test fold change filter to disregard the scale of the data (logged or unlogged), so that now when the data is logged the difference is compared against log2(Threshold) instead of comparing the ration against the threshold Version 6.06 additions ========================= 1) Updated organism data for all supported species (including chromosomal location information for tomato) 2) Improved coloring scheme for enrichment histograms 3) An option to change column color in histogram by clicking on the color icon in the color index. 4) Improved cluster homogeneity calculation by changing it from mean similarity to center to mean pairwise similarity 5) Added chip common cdf files to organism specific data to facilitate cel file preprocessing 6) Fixed bug in using Analysis Wizard with organism "Other" 7) Added key reaction to dialog boxes Version 6.07 additions: ========================= 1) Wiki-Pathway based group analysis option added (including data for 9 organisms for which wiki provided pathway information) 2) Automatic installation of all required R packages upon trying to activate tools for which packages are missing (with the acception of chip specific CDF packages). 3) Correction of bug preventing the dipslay of KEGG enrichment results from being overlayed on the corresponding web map correctly 4) Ability to load multiple condition attributes (i.e. classes/annotations) in a separate file. These can later be presented under the heat map that is displayed after hierarchical clustering. Version 6.1 additions: ========================= 1)Wiki-pathways based enrichment analysis 2) Automatic installation of required R scripts 3) An option to load multiple labels for experimental condition annotations Version 6.2 additions: ======================= 1) Gene Sets Enrichment Analysis (GSEA) 2) Integration of Amadeus tool for motif discovery 3) Correction for t-test bug and addition of t-value column in t-test results Version 6.3 additions: ====================== 1) A "save all" option which allows to export all open solutions to text and image files 2) FDR correction added to GSEA 3) Option to run GSEA on WikiPathways or KEGG data 4) Option to run GSEA on a pre-defined ranked gene list with no associated gene expression data (via File>>New Session) 5) Menu organization improvements