DAnTE Revision history: ______________________ Changes in Version 1.2: _______________________ September 02, 2009: ------------------ - Added a command line option "-u" to turn on the updating of R packages. By default this will be turned off now. This will take care of some user priviledge issues. Aug 10, 2009: ------------ - Fixed a bug that showed 'Score' column in plotting of new Rollup results. Aug 6, 2009: ----------- - Fixed a bug for Vista - Added Protein scores - Added one sample t-test - Added logging (-l -f ) July 29, 2009: ------------- - Rollup via top specified number of peptides is added as an option in QRollup procedure (as per Kim Hixson) May 06, 2009: ------------- - Fixed to work on Microsoft 64bit platforms (Vista, Windows 2003 server etc). April 08, 2009: -------------- - Fixed to run with latest release of R and statconnDCOM March 27, 2009: -------------- - Heatmap cluster color ranges added. - Memorizing the color pallette - Scatter plots on correlations now show number of points and LOESS curve - Instead of Rscripts folder, DAnTE.RData file added - R scripts were broken into pieces and organized - temp folder was changed to writable Common Applications Setting folder January 20, 2009: ---------------- - Added deletion of datasets - Tracking and saving parameters in analysis steps Changes in Version 1.0: _______________________ July 22, 2008: ------------- - Cairo devices are used for plotting which gives better quality. July 01, 2008: ------------- - Multiple 'Filtered Data' tables. - Venn Diagram plotting. Jun 27, 2008: ------------ - Fixed a bug in imputation methods when applied to factor levels. - Median Absolute Deviation (MAD) can now be applied on factor levels, not just globally. June 16, 2008: ------------- - Fold change calculations updated to handle log as well as non-log data. - updated the PNNL DMS connectivity to retrieve SEQUEST results files. May 10, 2008: ------------ - Fold change calculations. - Fixed an issue with auto scaling of rows in heatmap plotting. April 08, 2008: -------------- - Added a missing value filter - Major rewrite on the structure of DAnTE. March 28, 2008: -------------- - Merging columns of data tables based on a selected factor is added. - Few choices for loading SEQUEST out files are added. March 11, 2008: -------------- - DAnTE can now handle peptide count data - Clustering assignments/order from the heatmap plot is displayed in a data table January 31, 2008: ----------------- - Shapiro-Wilks Test for normality check - Non-parametric tests * Wilcoxon test * Kruskal-Walis test - PCA and PLS now reports p-values corresponding to the weights - QQ Plots - Updates to p-value filters - Several distance metrics and linkage methods to Hierarchical clustering - Updates to K-means clustering (now uses the R package 'amap') - Documentation updated - Fixed a bug in gridview context menu (right click on column headers) Changes in Version 0.86: _______________________ December 04, 2007: ----------------- - Added a context menu for plotting single/multiple rows of datatables. November 30, 2007: ----------------- - Added dataset feature counts to boxplots. November 28, 2007: ----------------- - A bug in the ZRollup method was fixed - Dataset names in the rollup plots can be turned on/off now. This will take care of long names overlaping the plots. Changes in Version 0.85: _______________________ October 29, 2007: ---------------- - Heatmap plotting with Hierarchical dendrograms and/or k-means clusters - Replaced GridData control by the .NET 2.0 control GridDataView Changes in Version 0.82: _______________________ October 23, 2007: ---------------- - ANOVA methods (n-Way, unbalanced designs, random effects) Changes in Version 0.80: _______________________ October 04, 2007: ---------------- - Converted to MDI (multiple document interface) Changes in Version 0.70: _______________________ September 28, 2007: ------------------ - Partial Least Squares - Reading Excel files with multiple sheets - Quantile normalization - Replotting feature from Plots - Adding a Data/Name stamp to each plot - Few bug fixes September 17, 2007: ------------------ - log2 and log10 with a bias term - PCA loads, percent variation etc - More options for PCA bi-plots - Black-body color scheme, and more options for correlation plots - Working folder saved and used throughout a session - Multiple plot windows can be opened simulteneously - Print/Print preview from plots - Save user modified color palettes between sessions - Boxplot coloring based on factors August 16, 2007: --------------- - Improved outlier test for protein rollups (now this will remove multiple outliers within the p-value cutoff) - Saving to tab-delimited files in addition to csv (for convenient loading to MeV) - a major bug fix in correlation range selected plots - Detailed help file August 08, 2007: --------------- - Linear Regression - Reference data set options for LOESS and Linear regression normalizations - MAD adjustment - Updated rollup methods - Toolbar updates - Correlation range selection for Correlation plots - Scaled data matrix is available for reference peptide based scaling Changes in Version 0.35: _______________________ July 24, 2007: ------------- - Protein rollups (Reference peptide based and Qrollup style) - Mean Centering data - Context menu for saving a grid with protein IDs - PCA plots - Temp file clearing option in Tools menu Changes in Version 0.30: _______________________ July 11, 2007: ------------- - Factor definition (add/remove/save) - LOESS normalization - MA plots Changes in Version 0.20: _______________________ June 28, 2007: ------------- - Plotting peptide-protein rollup/scaling data (Medain/StdDev method) June 27, 2007: ------------- - Peptide Scaling. - Rolling up to proteins. - Peptide/protein plots. Changes in Version 0.17: _______________________ June 4, 2007: ------------ - Plotting functions - histograms, boxplots, correlation heatmaps.