Scaffold LFQ Release Notes

The following document contains release notes for Scaffold LFQ

Scaffold LFQ Version 4.0.2 (Released 2021-09-17)

Restored functionality of sample clustering in the heatmap

Changed background coloring of Protein # column header in Samples View

Scaffold LFQ Version 4.0.1 (Released 2021-03-18)

Added a "clear" button to the advanced filter dialog

Added tooltips to the column header in the Proteins view peptides table

Added support for FDR thresholding of MZID data using Percolator PEP or Byonic scores

Added a helpful message when an already-expired key is activated

Added drag-and-drop in the license entry dialog

Allow pasting or dropping License ID and Password at the same time in the license entry dialog

Allow assigning attributes by dragging an attribute folder onto a sample

Added feature to include current License ID when reporting errors

Show more detailed messages in the progress dialog

Added ability to copy selected text from the publish view

Added tooltips to violin plots

Updated colors, icons and GUI look-and-feel for Scaffold LFQ

Improved functionality of the volcano, quantitative scatter and PCA scores plots

Improved performance for internal utility methods

Improved some error messages when reading an invalid MZID file

Improved handling of file paths in an MZID when they are URL-encoded or contain special characters

Switched to bundling Java 11 JRE in installers

Improved GUI behavior in the bulk edit sample names dialog

Replaced "MZID-specified" with "externally-specified" in grouping and thresholding UI

Updated default locations for some image exports and attribute file export

Updated the Samples view color legend when switching "log intensities"

Fixed "No Clustering" optimization that could cause some groups that passed thresholds to not display

Fixed an infinite loop when trying to draw a box plot with few underlying items

Properly display percentage values in the color options dialog

Fixed incorrect scrolling to selected peptides in very long protein sequences

Fixed graphical artifacts in the protein sequence panel when resizing the window

Prevent the Proteins view from displaying filtered-out proteins

Report the cutoff for decreasing scores unambiguously in the publish view

Fixed bug in the summarization combo box that could prevent editing summarization

Corrected typo in installation error message

Fixed protein selection dropdown options after double-clicking a protein in the volcano plot

Fixed a bug causing the GO Term Filter to not appear when first applying GO terms

Fixed a bug that could cause incorrect normalization of counts for the selected protein after changing summarization or statistical test

Fixed a bug that could cause GO term clustering to randomly fail

Fixed a bug which could cause an error while recomputing heatmap clustering; improve performance of heatmap rebuilds

Fixed a bug that prevented proper opening of files when an attribute category's name contained leading or trailing whitespace

Fixed issues with cut-off text and keyboard focus traversal in the license entry dialog

Ensure that tooltips in quant trend charts correctly respect the "Log Intensities" option

Fixed a hang when copying an EMF image from the PCA scores plot

Fixed resizing of the Organize view when deleting a category; ensure buttons are consistently sized

Fixed a bug when imputing quantitative values with certain sample counts

Fixed an error when sample names contained long sequences of digits

Display group names in volcano plot tooltips instead of "null"

Do not show multiple rows for a protein group in the heatmap details

Do not display GO Terms that are associated with a protein with the "NOT" qualifier

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