1.4.0 Release Notes

Highlights

  • Introducing a Clustering Platform – Now available in the Discovery band of the Workspace, which allows researchers to run KMeans clustering and KNearest-Neighbors (KNN) classification.
  • Genes illustrated in the Pivot Window (i.e. Gene View) can now be selected and filtered in the top left hand corner of the Graph Window. This allows researchers to focus only on parameters of interest when gating in Gene View.

Improvements

  • PCA now contains options to normalize and log transform parameters used for the dimensionality reduction, greatly improving the resulting clustering.
  • Optimizations to the tSNE algorithm to increase efficiency of the calculation.
  • Support for sparse expression matrix “.st” file types.
  • Support for synthetic parameters, such as GeneSets, in multigraph color maps.
  • Release notification mechanism to let users know when the next release becomes available. (Active for releases post SeqGeq v1.4.0)

Fixes

  • Adjustments to p-value calculations in volcano plots.
  • Axes labels for Gene View plots in the Layout Editor can now be edited from the Graph Definition window.

Known Issues

  • Identically named population will not behave as intended in Gene View. Workaround: Name all populations uniquely.
  • 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.
  • Changes to Gene View dot sizes are not saved. Workaround: Adjust dot sizes in the Display tab of the Graph Window.
  • Bring forward command in Layout Editor gives bug reporting window. Workaround: Close the bug report window and continue analysis.
  • 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.

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