What's new in GProX 1.1.13
May 9, 2014
- Fixed problem updating/installing R packages
New in GProX 1.1.12 (Aug 12, 2013)
- Fixed problem updating R packages
New in GProX 1.1.11 (Aug 12, 2013)
- Fixed problem with enrichment test using BH correction
New in GProX 1.1.10 (Aug 12, 2013)
- Fixed bug which made it impossible to retrieve GO terms from UniProt
New in GProX 1.1.9 (Aug 12, 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.
New in GProX 1.1.8 (Aug 12, 2013)
- 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.
New in GProX 1.1.7 (Aug 12, 2013)
- Bugfixes:
- 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.
New in GProX 1.1.6 (Aug 12, 2013)
- Bugfixes:
- 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.
New in GProX 1.1.5 (Aug 12, 2013)
- 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:
- 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.
New in GProX 1.1.4 (Aug 12, 2013)
- New features/Changes:
- The query database and pathway analysis now accepts Ensembl Gene IDs and Ensembl Protein IDs
- Bugfixes:
- 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.
New in GProX 1.1.3 (Aug 12, 2013)
- Bugfixes:
- 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.
New in GProX 1.1.2 (Aug 12, 2013)
- New features/Changes:
- New option in heatmap plotting to select which proteins to include in plot.
- Bugfixes:
- 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.