Highlights

• Introducing a Quality Control button yielding QC parameters in both Cell and Gene Views within the Graph Window.
• Volcano Plots available from Gene View, for calculating statistically significant Differentially Expressed Genes.
• Dimensionality Reduction Parameter Vector Inspector platform.
• Added Rank and Quantile plot types.

Improvements

• Enhanced performance.
• Searchable parameter selector within the Add Statistics dialog.
• “T” buttons enabled in Gene View Graph Windows.
• Ranges added to color mapping key in color mapped plots within the Layout Editor.
• Quadrant gating tools added to the Graph Window.
• New and Demo Data from Illumina’s SureCell platform, 6k PBMCs from 5 samples. Synchronizes with tutorial.

Fixes

• “Export Eigen Vectors” will now output a CSV file containing vectors from PCA to the user’s chosen directory.
• Color mapping parameter key will no longer be able to overlap x-axis parameter.
• Histograms now allowed in gene view.
• Gene Sets now update live within the Graph Window.

Known Issues

• Legacy workspaces with gates drawn in Gene View will need to be re-confirmed, as changes in this version may have altered their position or geometry.
• “Export Eigen Vectors” button from Principal Component type Dimensionality Reduction dialog for Windows will default to save the vectors in a temporary forlder. Workaround: Make sure to save vectors to a common location, such as Desktop.
• Changing the scale of parameters in Gene View Graph Windows to Linear with a minimum value ‘zero’ is known to cause exceptions. Workaround: For this release, we recommend not utilizing this range bound in that plot type.
• Changes to Gene View dot sizes are not saved. Workaround: Adjust dot sizes in the Display tab of the Graph Window.
• Changing transforms can result in line of co-expression falling in an incorrect position. Workaround: Re-select either axis parameter to refresh this feature.
• Synthetic parameter (e.g. a gene set in Cell View) transforms are not saved in GeqZip.
• Bring forward command in Layout Editor gives bug reporting window. Workaround: Close the bug report window and continue analysis.
• Mousing over coordinates in volcano plot illustrates fold change ratio (x-axis coordinate), rather than the raw value.
• Derived Observations (e.g. PCA vectors) calculated for certain Derived Parameters (e.g. a Gene Set in Cell View) will not be correctly applied when re-opening a saved analyses. Workaround: Don’t apply Derived Observations to Derived Parameters.
• Only demo data can be loaded when running SeqGeq in demo mode; i.e. concatenated data (even from demo files) cannot be loaded into SeqGeq in demo mode.
• Some hotkeys meant to open tabs in the Workspace will generate a bug report window.
• Bug reporting window does not send information to FlowJo, LLC. Workaround: Send an email to tech support for a speedy reply and troubleshooting: seqgeq@flowjo.com
• The 24 hour authentication grace period for temporary offline access will sometimes fail to correctly activate.
• Running tSNE on a raw expression matrix is not advised. Workaround: We recommend running tSNE on principal components, after running PCA on the expression matrix of interest.
• On a Mac, R-based plugins fail to calculate if the file paths contains a space or other special characters. Workaround: Remove spaces and special characters from file paths associated with the analysis.
• DRP wait time warning messages are overly conservative and need recalibration.

If you have any questions or comments regarding the SeqGeq platform we greatly appreciate any feedback.