PGS Documentation

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To install or upgrade to the latest version of Partek® Genomics Suite™ software, follow the directions outlined in the Installation Guide.

PGS7.18.0723

General Improvement:

  • Microarray methylation workflow to make it more intuitive

Bug fixes:

  • Minor bug fixes

PGS7.18.0518

General Improvement:

  • Implemented DMRCate algorithm for differential methylated regions detection
  • Added false discovery rate report in html format
  • Add options to delete rows contains missing value only during text import

Bug fixes:

  • Minor bug fixes

PGS7.18.0402

General Improvement:

  • Sped up multidimensional scaling function
  • Added chi-square analysis for categorical data
  • Improved Fisher exact test on integer columns with two distinct values
  • Improved handling beta value as 0 or 1 during M value transformation, instead of output "?", we set the value as 1e-6 or 9e-6 by default

Bug fixes:

  • Fixed GEO downloader issue
  • Fixed scatterplot set cutoff line and regression line button issue
  • Fixed a dot plot close issue
  • Bug fixes on OSX

PGS7.18.0130

General Improvement:

  • Improved the methylation workflow – add region methylation analysis workflow
  • Added correlation analysis across two spreadsheets when they have the same set of samples

Bug fixes:

  • Bug fixes on OSX

PGS7.17.1222

General Improvement:

  • Improved the ANOVA contrast dialog; added the option to output difference between the two groups instead of fold change
  • Added new options on the Illumina methylation array importer to allow filtering of probes based on detection p-value and XY chromosomes
  • Improved Illumina methylation array analysis workflow to compute differential methylation sites based on M value and report the difference of M and beta values

Bug fixes:

  • Fix Tk event crashes on OSX
  • Other minor bug fixes

PGS7.17.1103

General Improvement:

  • Sped up genome view with large annotation files
  • Added option to specify output file name on task dialogs
  • Added option to save merged spreadsheet to a new spreadsheet

Bug fixes:

  • Fixed a hierarchical clustering viewer bug on Mac version
  • Other minor bug fixes

PGS7.17.1018

General Improvement:

  • Partek spreadsheet can only be saved as binary format
  • Partek spreadsheet can be exported as text format. The name of the exported spreadsheet will not be changed
  • "Import Text File" will not change the input text file, the imported file will be saved as user-defined name in binary format
  • When there are unsaved spreadsheets, "Save Project..." and "Export Zipped Project..." will give a warning message to save each unsaved spreadsheet
  • When cloning a spreadsheet, the newly generated spreadsheet name is unique by default
  • Re-ordered the File menu to improve usability
  • Added a function to impute missing values with random numbers from a defined distribution
  • Improved the "Save Image As..." dialog on Mac and Linux
  • Added support for save image as JPEG on Mac and Linux
  • Added file type selector for open and save file dialogs on Mac
  • Violin Plot displays the properties tab by default 
  • Gene Expression workflow "Import from Affymetrix CEL Files" and File menu "Import Affymetrix .CEL Files" produce the same output spreadsheet for gene expression arrays
  • Improved graphics for visualizations on Mac

Bug fixes:

  • Fixed a bug on "Split Column" dialog on Mac
  • Fixed a bug in "Import Affymetrix .ARR File..."
  • Other minor bug fixes

PGS7.17.0918

General Improvement:

  • Most of the computations are multi-threaded, which drastically increases the speed
  • Viewers generated from spreadsheets are new tabs within the same window frame by default; viewer windows can be docked back to the main window frame
  • Workflow panel is visible in any invoked viewers, order of the workflow steps is more intuitive
  • Updated with modern icons and graphics color palette
  • Mixed model ANOVA uses REML by default
  • Sample ID factor is not included in the model of Alt-splicing ANOVA, GO ANOVA, pathway ANOVA
  • Apply button are removed from most of the dialogs
  • Improved interface is cleaner and more user friendly
  • New functional normalization method in the Illumina methylation array importer (450K and 850K)
  • Improved SWAN normalization in the Illumina methylation array importer
  • Allows import of different versions of the Illumina methylation arrays when using the same set of library files
  • Improved text file importer by adding wizard for specifying the properties of the spreadsheet
  • Removed repeated measures menu option, it is recommended to use ANOVA doing repeated measures analysis
  • Simplified menus and dialogs, removed obsolete functions, improved wording
  • Automatically downloads annotation files, even from sites with HTTPS or redirects (e.g. Affymetrix and GEO)
  • Logged data is detected and appropriate defaults are automatically set

 

Older release notes are available on our website at Partek® Genomics Suite™ Software Update Archive.

 

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