Version History
Version 1.1.13 (08.05.2014)
- Fixed problem updating/installing R packages
Version 1.1.12 (05.08.2013)
- Fixed problem updating R packages
Version 1.1.11 (02.08.2013)
- Fixed problem with enrichment test using BH correction
Version 1.1.10 (18.07.2013)
- Fixed bug which made it impossible to retrieve GO terms from UniProt
Version 1.1.9 (02.05.2013)
- Re-enabled KEGG pathway analysis functionalities. To implement this all users are now requested to update R to version 3.x.x.
- Disabled database query function for IPI accession keys due to the closure of the IPI database.
- Fixed the IPI acession key update to allow updating IPI keys to the final version and fixed bug when attempting to update Reverse or contaminant keys.
- Made Uniprot the default acession key selection.
- Updated tutorial.
Version 1.1.8 (27.03.2012)
- Fixed a bug that made the program fail in cluster analysis if the session was in a folder called txt (such as MaxQuant output).
- Modified enrichment analysis so that the number of terms are now drawn from the number of proteins and not as previously from the total sum of terms. this seems to be a more widespread approach.
- Several changes on the R side have unfurtunatelly made it necessary to temporarily disable the pathway analysis feature. We hope to be able to reactivate this soon.
Version 1.1.7 (23.11.2011)
Bugfixes
The following issues has been resolved:
- Due to changes in the policy for add-in libraries for R, these had to be rebuild for R version 2.14.0. This prevented older versions of GProX packages to be loaded in R v. 2.14.0, giving a 'no namespace' error message in the Session log.
- Secondary accession keys no longer appear in the column selction boxes for redefining experiments.
- Deleted experiments can no longer be selected in the drop-drown boxes in the redefine experiments dialog.
- Pasting values from spreadsheet program into GProX session table gave index out of bounds error.
- During data import a warning is given if the input table contains columns with blank headers inside the data table.
- Column selected in session table is also selected in column rename dialog.
- When specifying a lowest rank for GO analysis only GOBP terms was screened in previous versions, now also GOCC and GOMF terms are screened.
Version 1.1.6 (26.10.2011)
Bugfixes
The following issues has been resolved:
- There is a serious bug present in all previous GProX versions, which
leads to loss of all files in the folder containing the input file, if
no "Session name" is given during data import. This would result in
the session folder being the same as the folder containing the input
file, and if accepting to overwrite this folder, would delete all
files in the folder containing the input file.
Version 1.1.5 (07.10.2011)
New features/Changes
- New option to plot data density histograms or boxplots in margins of scatter plots.
- New option to make scatter plot points transparent.
- New option to include gridlines in scatter plots.
- New option to disable trendline in scatter plot.
- Included option to center heatmap color scale on zero.
Bugfixes
The following issues has been resolved:
- Filter function for cluster and enrichment analysis treated multiple terms as OR conditions although specifying them as AND conditions.
- Automatic download of R could fail if the R webpage was not updated.
- Selected columns in scatter points were not reset when loading a new session.
Version 1.1.4 (17.08.2011)
New features/Changes
- The query database and pathway analysis now accepts Ensembl Gene IDs and Ensembl Protein IDs
Bugfixes
The following issues has been resolved:
- Wrong assignment as regulated could occur for non-regulated proteins.
- Histogram plotting could fail with very extreme values.
- Columns in input table with an empty header cell are ignored during data import.
- Column headers are checked During data import to ensure that all headers are unique.
- Warning if trying to plot experiment ratios with only 1 datapoint.
- Disabled adding columns not present in all data tables to experiment. Could cause exception.
Version 1.1.3 (29.07.2011)
Bugfixes
The following issues has been resolved:
- Wrong mapping of ratio to nodes could occur if several isoforms for a node is present in the data table.
- Behavior of user interface drop-down menues improved.
Version 1.1.2 (15.07.2011)
New features/Changes
- New option in heatmap plotting to select which proteins to include in plot.
Bugfixes
The following issues has been resolved:
- Pathway analysis was not working because the KEGG data structure was changed as of 1 of July 2011.
- All file format versions of graphics was not removed when deleting graphic objects.
Version 1.1.1 (14.07.2011)
Bugfixes
The following issues has been resolved:
- The check for special characters in the input file name was too restrictive. Changed so white space " " and dash "-" are allowed.
- Undo/Redo still enabled when starting or loading another session.
- The 'Filter for most descriptive terms' function was only functional for GOBP terms. This has been changed so it now works with both GOBP, GOMF and GOCC terms.
Version 1.1.0 (15.06.2011)
New features/Changes
- Graphical summary of cluster analysis
- To improve the layout when many clusters are requested the arrangement and font sizes has been made more sensible. Due to these changes the number of clusters have been limited to max 22.
- Histogram of the number of proteins in each cluster included.
- Paramters are included in output.
- Modified layout of color key. These changes release the requirement for the marray R package.
- Parameters for enrichment analysis included in heatmap visualization.
- Scaling of row labels in heatmap from enrichment analysis and heatmap plots improved to avoid overlapping labels.
- Cancel option included in the 'Select filename' dialog.
- Title and link to the GProX publication provided in the about window.
- Open recent file function added to welcome screen.
Bugfixes
The following issues has been resolved:
- Table sorting directly after inserting blank column caused crash.
- Database querying for information already in table and selecting not to overwrite could cause crash.
- Selecting fonts not available could give
exception.
- 'integerSortCol' used for numerical sorting was included as a selectable column in dialogs.
- Window selection menu disabled if starting new window. Selecting windows after opening wizard gave exception.
- Density scatter plot pixel size was ignored.
- Program was not closed when the top right X was clicked and the process had to be terminated from the task manager. Hopefully, this has been solved now.
- No x-axis labels on stacked histograms.
- Updated list of available database annotations available from Ensembl.
- Session tables not saved after moving rows to new table or appending causing these rows to still be included in analysis steps.
- Cluster analysis with to few proteins gave error. New sanity checks included.
- Lowest rank in enrichment analysis limited to 3. Selecting more than this makes analysis times extremely long.
- Enrichment analysis. New sanity check that data grouping has been selected.
- File not found error it scatter plots with the same column on both axes were requested.
- To avoid subseqeunt problems the input filename is checked for special characters.
- No 'Save changes' dialog displayed when closing and only the input wizard is open.
- No 'Save changes' dialog displayed when opening old session and only the input wizard is open.
- Repeated 'Update package' dialog displayed if GProX packages were in different R libraries.
- Retrieve components dialog resize correctly if session windows is maximized.
Version 1.0.2 (23.05.2011)
Bugfixes
The following issues has been resolved:
- Clustering analysis failing due to insufficient privileges to write to directory for temporary files.
- Enrichment analysis failing if only one term was found significant.
- During data import column names are checked to ensure that the first character is letter to keep R happy.
- Reporting the first name for all Pfam ids in enrichment analysis.
- Additional checks to ensure unique column names.
Version 1.0.1 (17.01.2011)
Bugfixes
The following issues has been resolved:
- Error when session table contains exactly 101, 201, 301 etc. entries.
- Problem overwriting protein plots.
- Wrong input to input wizard could cause unhandled exception.
- Problem generating stacked histograms.
- Missing close button on peptide filtering for IPI keys update.
Version 1.0.0 (31.12.2010)
Major Revision
- Complete rebuild of the user interface.
- All R packages has been collected in the R libraries GProXutil, GProXplot and GProXanalysis
- Added support for Windows 7 64 bit
Version 0.9.9 (3.6.2010)
Bugfixes
The following issues has been resolved:
- Problems getting the list of KEGG pathways
- The last line might have been removed
- Column header in two-way enrichment test was reversed
- Message is given if the BioMart service is temporarily down
- Messages are now given if the selection is incorrect for column delete, average columns and plot protein
Version 0.9.8 (3.5.2010)
New features/Changes
- Tutorial added, this can be started from the welcome screen
- Tootip help has been placed for most parameters
- R installer is downloaded to GProX files folder in MyDocuments
- GProX will always install the newest R version
- Check for new GProX version is executed as external process to make startup faster
- Input file is only displayed after import if selected to decrease startup time
Bugfixes
The following issues has been resolved:
- Undo caused unhandled exeption
- Renaming graphics to already existing file gave exeption
- White spaces in experiment names gave errors with consecutive clustering
- Error in orgism specification made pathway mapping defunct for all species except human
- Problem with work directory in R-2.11.0 may cause clustering to fail
Version 0.9.7 (26.3.2010)
New features/Changes
- Tabular output for pathway analysis
- Entrez gene identifiers present in the Data table can be used to mapping to pathways.
- Automatic startup check for relaease of new version
- 'Get database sheet' functions other than input now always return the first entry.
- Additional functions has been added to the Data Tables right-click menu.
- Multiple columns can be selected for on-the-fly Histograms, Heatmap, boxplots etc.
- Additional 'sanity check' for correct installation of R has been included.
- Color customization options of graphical cluster output has been increased.
- To comply with Windows 7 security settings, log file is saved to GProX files folder in MyDocuments
Bugfixes
The following issues has been resolved:
- Pathway selectionlist not loaded correctly.
- Enrichment test barplot returned onsensible values.
- Errors in protein plot titles if one ore more entries did not contain any data.
- No result by querying databses with alternative accession key column if alternitice and primary source was the the same.
- Warning is given if one or more clusters only contain one entry.
Version 0.9.6 (12.3.2010
New features/Changes
- Support for Windows 7 32-bit OS.
- New feature for plotting data as heatmap.
- Retrieve components improved and reorganized.
- Presence of all required R packages and regional settings are checked at startup.
- The presence of a protein in a pathway selected for analysis is written to the Session Table.
- Color key is included in clustering graphics.
- Colors for clustering graphics can be customized.
- Added a number of sanity checks to selection boxes.
- Graphics files can be renamed.
- Help file updated.
Bugfixes
The following issues has been resolved:
- Problem with changed output from the biomaRt package caused retrieval from Ensembl to return blank columns
- Wrong matchstring for retrieval of gene names from uniprot.
- Local copy of Session Info saved after redefining experiments.
- Warning that directory exists is no longer written so session log.
- Wrong reference to local folder causing problems if user did not have a folder 'c:\temp.
- Error occured with consecutive clustering.
- Error if clustering data did not contain any 'n/a' or cluster 0 entries.
Version 0.9.4 (19.2.2010)
New features
The following issues has been resolved:
- Support for users connecting to the internet via a proxy server
- Copy/Cut/Paste functionalities implemented
- Histograms of multiple data-series, stacked or juxtaposed
- Browse session folder function
Bugfixes
- Wrong lines selected for new table
- Lines skipped for protein plot
- IPI update crash if no sec. acc. keys