This article lists the most important changes made in Coffalyser.Net v.210604.1451 and v.210226.1433.
||These are not the latest versions of Coffalyser.Net. See the version history for information about other (newer) versions.|
||Coffalyser.Net v.210604.1451 and v.210226.1433 only differ in the installation procedure. There is no need to update to v.210604.1451 if you already have v.210226.1433 installed.|
The sections below list the changes as compared to the previous version, v.140721.1958.
Most prominently visible improvements
- Improved workflow for manual bin set creation.
- Adjusted probe counter to make a clear distinction between expected probe signals and unexpected probe signals. More details.
- Added probe colours in the genomic profile tab of the fragment analysis and electropherograms tab of the comparative analysis for improved visualisation and identification of unexpected results. More details.
- Added purple colours to binning profiles to identify probes that deviate too much from the center of a bin. More details.
- Added support for the Applied Biosystems SeqStudio Genetic Analyzer and the Promega Spectrum Compact capillary electrophoresis devices.
- Updated default Microsoft SQL Server from 2008 R2 to 2014 SP3 to help prevent possible future security issues with SQL Server and to increase compatibility with modern systems.
- Improved support for Windows 10 (32- and 64-bit). View all system requirements.
Improvements to quality scores
- Added a max probe length deviation quality check to the FMRS score to provide warning if a probe fragment length is too far removed from the center of a bin. More details.
- Added FMRS score penalties if the 92 nt benchmark fragment is not within an appropriate signal range. This includes a heavy FMRS score penalty if the benchmark fragment is absent but expected, to avoid a potential overestimation of quality because some quality checks cannot be calculated without the benchmark fragment.
- Added the possibility for the PSLP score to become red/bad and lead to an increased penalty for the CAS score if there are large differences in sloping.
- Added an FMRS score penalty for undetected probes in undigested reference samples in MS-MLPA.
- Added a CAS score penalty for test samples when signals in the experiment's dedicated reference samples are out of range.
- Adjusted the way that results for probes with a signal ≤ 10% of the median signal of the reference probes are displayed. Results for these probes are now displayed as intra-normalised ratio (as percentage) in all tables to enhance the visibility of unexpectedly low signals. Results for probes with a higher signal (> 10%) are still displayed as final ratios.
- Improved automatic bin boundaries for mutation-specific probes that are not identified in the experiment. These bins now become wider by default to increase the chance of detection of positive signals. A manual bin set and SALSA Binning DNA should be used to avoid this situation.
- Adjusted minimum signal height for filtering from 5,000 to 3,000 for Beckman devices.
- Adjusted mapview locations to display the approximate location of probes.
- Adjusted default region analysis method, which will be set to StaticMRCData if available. When not available, this option is no longer shown in menus.
- Improved fit of information displayed in tooltips to the screen.
- Improved visibility of information about mutations in PDF reports.
- Improved consistency in available zoom options throughout the software.
- Improved layout of the sample information displayed at the top of PDF reports.
- Removed outdated, non-functional links to the reference manual and YouTube channel.
- Removed comparison of samples to the overall sample population and to the positive sample population throughout the software.
- Removed intra-normalisation ratios throughout the software.
- Removed two unused, non-functional conditional format options from menus: PeakDeltaNucleotideExpectedLength and PeakWidthInDataPoints.
- Removed normal range from PDF reports as they did not apply to all situations.
- Removed "DNA" check for no-DNA reactions as it had limited value.
- Updated information in the About dialog.
- Added support for a potential future alternative approach to MS-MLPA (referred to as unpaired MS-MLPA in the software).
- Fixed inconsistent display of results for mutation-specific probes. Previously, results in the Sample report tab of the Comparative Analysis Sample Results Explorer could be displayed differently than in other places in the software in certain situations.
- Fixed gender determination in the absence of the 92 nt benchmark fragment in the fragment analysis tab.
- Fixed inconsistent display of PSLP warnings in dialogs and PDF reports.
- Fixed inconsistent display of FRSS scores in some situations.
- Fixed an exception and inability to view all results when a digested sample had a signal for a probe without signal in the undigested reaction in MS-MLPA.
- Fixed an exception and inability to generate PDF reports when the length of text describing the reference samples on PDF reports was exactly 91 characters.
- Fixed rare conditions in which peaks could be assigned a negative area.
- Fixed rare situations in which changes to the fragment analysis configuration did not reset the comparative analysis.
- Fixed incorrect slope correction warning when no slope correction was applied.
- Fixed incorrect warning for incomplete digestion for experiments not analysed as MS-MLPA experiment.
- Fixed incorrect last modified date for experiments.
- Fixed absence of altered formatting to warn for large probe fragment length deviations from the center of a bin in PDF reports and tables in certain situations.
- Fixed layout of PDF reports in the absence of chromosomal band information for probes (only relevant for custom probemixes).
- Fixed inconsistent rounding rules for result ratio calling and displayed values.
As compared to v.210226.1433, two changes were made to improve the installation procedure. No other changes were made.
- Improved handling of aborted or interrupted installation of Microsoft SQL Server.
- Fixed an issue with computer names containing Unicode (UTF-8) characters.
||Coffalyser.Net v.210226.1433 was made available on our website on 26 May 2021. Coffalyser.Net v.210604.1451 was made available on our website on 10 June 2021. Coffalyser.Net version history.|