Version History
Version
Log
Release Date
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0.4.1
New Features
- Columns can be filtered (included or removed) in Export Tables feature;
- The program now guesses if a matrix is already in log2 scale and accordingly checks options related to log2 application by default.
Bug Fixes and Adjustments
- Tables viewed from any full table view dialog are now exported exactly as displayed (i.e., in the same order and with the visible columns only);
- Fixed the 'object comparison_main' error from multiple comparisons;
- Removed the "ghost" group that appeared upon entering the multiple comparison section;
- Tooltips with the expanded name and status now appear in the Platform Selection dialog when the name overflows;
- Optimized the sample metadata download when loading a single series entry;
- More specific error messages for internet connection issues;
- Variable precision when setting numeriv values, especially for logFC and p-values;
- Groups from multiple comparisons can now be renamed;
- Ctrl + Left/Right arrow keys can not be used to distribute samples between sample groups;
- Negative values are not removed from matrices anymore if they are in log2 scale;
- Fixed the startup fail ("Could not find R executable") when running GEAP from a different directory;
- Added "Non-coding RNA profiling by array" in the list of supported array types, as GEAP already supports some platforms employing this technology;
- Fixed RAW data inclusion when exporting RDS and RData.
03/13/2022
0.4.0
New Features
- Custom tables now can include dual-channel and background detection. A different set of statistical options are provided depending on the inclusion of background signals or channels;
- Series Metadata Editor for custom tables. Now, dataset descriptions can be appended to the custom tables and loaded as part of the session;
- Advanced selection options for sample distribution, such as "Select Inverse", "Select Odd", "Select Even", among other actions. In addition, by holding Ctrl, Alt, or Shift, the next sample selection will be included, excluded, or intersected from the current selection, respectively;
- Samples now can be selected and grouped by name patterns, such as wildcards (*) and regular expressions. The patterns are checked and matched with samples in real time;
- Added option to ignore certain lines that start with one or more prefixes when reading custom tables. This is particularly useful to ignore comment/metadata lines starting with '#' or '!', for instance;
- "Export tables" feature was restructured and now supports saving the datasets as CSV, GCT (Gene Cluster Text), and many other file formats. The previous export formats were also corrected and improved;
- Included several identifier options to reference genes in Gene Ontology analysis:
- Gene Symbol (same as "Symbol" in previous versions)
- Gene Name
- Gene Alias
- GenBank (same as "Accession" in previous versions)
- Ensembl
- Entrez
- RefSeq
- UniGene
- UniProt
- Support for GAF-derived Gene Ontology formats, including:
- FB (flybase.org)
- MGI (informatics.jax.org)
- RGD (rgd.mcw.edu)
- TAIR (arabidopsis.org)
- WB (wormbase.org)
- ZFIN (zfin.org)
- "Reload" button in the Series and Samples pre-analysis pages to (re)load and (re)apply statistical treatments on checked files from the previous session;
- Numeric values from Full Tables are displayed with full precision when their table cells are selected;
- Numeric columns in the tables of Differential Expression results now display a brief column description when hovering the mouse at a column header.
Bug Fixes and Adjustments
- Changed to R version 4.0.3;
- In "Full Table" dialogs, the columns' order and visibility are now preserved when alternating between different tables or applying filters;
- Removed extra row in summary table from single differential expression results;
- Optimized the image viewer (applicable to quality metrics and Gene Ontology results);
- Improved Gene Ontology graphics quality;
- FTP file list files are correctly addressed in the input files, instead of being considered a table file;
- Improved the dual-channel constraint option for sample lists. Now if both channels of the same sample are selected, only one channel is allocated to the target group;
- Fixed mismatches when merging probe attributes and differential expression results where the number of probes differ. This issue was present in certain Agilent platforms;
- Corrected the order between "Over" and "Under" columns in the summary table for multiple comparison results;
- Fixed independent interaction between "Select Folder" dialog and the parent window;
- Fixed freezing due to very long probe annotation fields by trimming the visible text. Applicable to dynamic plots from differential expression results;
- Fixed commas and decimal places when exporting multiple tables. Now the full precision is always used;
- Fixed unintended page change when cancelling the invalid value removal dialog before the quality metrics analysis;
- Fixed repeated documentation pop-ups when requesting help in some pages or forms;
- Some deprecated platforms are replaced by their newer versions (e.g., HuEx-1_0-st-v1 becomes HuEx-1_0-st-v2), so that their dependencies could be located;
- Added specific error messages for gene ontology analysis;
- Replaced the "FormatException: Could not find any recognizable digits" by the more self-explanatory message "Error while decompressing the file {filename.extension}". This error is caused due to corrupted ZIP/TAR files.
03/07/2021
0.3.2b
New Features
- NanoString RCC file support (TypeChecker add-on);
- Automatic merge of platform columns (GPL) to processed intensity table (GSE) based on the similarity between GPL columns and GSE row names.
Bug Fixes and Adjustments
- Fixed "minds == 0" error when row names are numeric;
- Fixed "missing values in row.names are not allowed" by removing the missing row names;
- Fixed "No such column: man_fsetid" error by providing the correct column. This adjustment allowed analyzing miRNA and lnRNA datasets;
- Solved the "The affy package is not designed for this array type" in Affymetrix datasets when using custom CDF by providing the correct CEL parser;
- Fixed fatal error (program crash) in platforms containing factor columns with NA values;
- Fixed "names must be a character vector" error by correctly converting integer-only row names to character;
- Fixed "there are more columns than expected" error by removing NA rows in misformatted files.
09/09/2020
0.3.2
New Features
- Custom CDF support to probe-level mapping in Affymetrix microarrays;
- Platform Design Info package support to more recent Affymetrix platforms. An "oligo" treatment option was added to this use case;
- MultiSOFT support: SOFT files containing multiple GEO entries can be read at once;
- R Source code generation (button available in Session Overview and Diff. Expression results page);
- TypeChecker can load Samples and Platforms in addition to Series as in previous versions.
Bug Fixes and Adjustments
- Updated R to version 3.6.3, as well as the underlying packages;
- Added ZIP to the file extension options during pre-analysis;
- Fixed processing bugs with older GenePix versions;
- Invalid values error fixed in arrayQualityMetrics when infinite values are present;
- Solved NullReferenceException in Export Dialog from Quality Analysis Results;
- Fixed "sample.int error" with some arrays using GC-RMA treatment method;
- Fixed unsaved filters when attempting to save Diff. Expression results in a Project;
- Fixed blank Library names just after saving the input files into the Library;
- Partially fixed dependency system for Library files, which didn't work for some data types. Further tests may be required;
- Transparent background glitch fixed.
07/16/2020
0.3.1
New Features
- Sequential DE analyses can now have multiple sequences (or "layers") of comparison. This way, multiple experimental conditions can be tested at once in a time-based study;
- Documentation is now available and can be accessed from Website and inside GEAP. There's a Help button at the bottom of the main window and at the top of any dialog window;
- "Stored Files" menu in the Session Overview to display the temporary directory tree;
- Full report of Quality Analysis results containing the figures' description. This report can be viewed or exported as HTML;
- Differential expression results are now automatically filtered. The filter can be configured in the Advanced Configurations section;
- The parameters used for RAW data treatment are now included in the Session metadata.
Bug Fixes and Adjustments
- Fixed the crash in Projects section, when trying to open another Project after fully loading a Session;
- Added constraint in GO panel to prevent starting the GO analysis when no attribute column is present;
- Fixed the crash when trying to access Samples and Session Overview sections in Portuguese language;
- Included the RAW paramaters from Agilent samples, which were missing due to a bug in data processing (now fixed);
- Corrected the grouping of Agilent samples from distinct platforms, avoiding the error caused by mixing them.
05/06/2020
0.3.0
New Features
- Full dual-channel support;
- Sample names are preceded by a circle indicating the label color;
- Samples have a "View As" option to display a sample attribute according to its metadata. This feature also works with metadata pairs in dual-channel arrays;
- Updating R Packages is now fully supported;
- Gene Ontology (GO) analysis for differentially expressed genes;
- Data Table Browser to explore both GSE and GPL matrices;
- SVG support for vectorial images, including plots;
- Added GPR support for GenePix microarrays;
- Added support for multifactor columns, whose cells are indexed and can have multiple fields. The fields are filtered separately when applying a filter;
- Custom table attribute columns can be loaded as multifactor columns if a separator is present.
- Attribute columns from results tables can be converted to multifactor columns.
- Display options for plot legends from differential expression analysis results. Legends can now be hidden or trimmed.
Bug Fixes and Adjustments
- Fixed the IO error when exporting a table from the Session Overview;
- Fixed library saving issues for Series, Samples and RAW;
- Fixed invalid requests to Bioconductor repository;
- Many other minor fixes and optimizations which would not need to be mentioned.
01/29/2020
0.2.0
New Features
- Type Checker as a new application to check, validate and process file types;
- Some of pre-analysis data, including Bioconductor packages list, are now cached, saving time when new analyses are needed;
- When sample information is available, sample names can be shown as any info field by right-clicking with mouse and choosing the desired info inside the 'show as' item;
- Multiple tries to connect internet and customized trying delay (useful for places with unstable internet connection);
- R console can be accessed through Tools → R Console;
- (Experimental) R Packages can be updated through Advanced Configurations → R Environment menu;
- Plotting and Web options are available in Advanced Configurations menu;
- Added 'Not Equals' conditional parameter to results filtering options;
- All plots can be exported as Enhanced MetaFile (EMF) and imported as vector images in editors like Adobe Illustrator, Corel Draw or Inkscape.
Bug Fixes and Adjustments
- Fixed translation and language issues in many parts of the application;
- GC-RMA required additional packages for statistical treatments. Fixed by adding a new option to download the missing package (checked by default);
- Fixed the process of saving raw data in library;
- Fixed sample information pane for Multiple and Sequential comparisons;
- Exporting results does not give NullReferenceException anymore;
- Mouse interaction with scatter and volcano plots is more precise now;
- Bar plots now display correctly when many groups are present. The labels also are resized according to the number of groups;
- Many other minor fixes and optimizations which would not need to be mentioned.
02/25/2019