Sometimes SeqGeq will inevitably fail to complete some tasks or to perform some function, especially for researchers who regularly push the envelope.

In these cases we try to include error messaging that conveys the issue(s) at hand in an informative and actionable way. Here are a list of common errors and a brief description of their causes.

File Loading

• “File contains data rows of varying length (a ragged matrix).”

SeqGeq does not support the loading of ragged data matrices; i.e. all cells must have values for all genes (and vis versa) – Even if those values are zero. As a workaround you can try to remove the genes or cells which don’t match the dimensions of the majority data matrix prior to loading into SeqGeq.

• “Invalid quote characters were detected.”

Quotes often identify string values (non-integer, non-float) within data matrices. In the case of this data file some quotes are improperly utilized.

File Merging

• “File could not be merged. The file contains cell IDs that are not present in the sample, and fewer than 10% of the sample’s cell IDs are present in the file.”

This indicates that a researcher has tried to merge a file in which less than 10% of the cell IDs are present with respect to the parent file, and which contains new Cell IDs not found in the sample. We currently require that at least 10% of a sample’s cells be represented in files merged with extraneous Cell Ids. As a workaround, if you know the subset of your sample which represents those cells you wish to merge, try exporting the subset, reimport it and attempt the merge again. You should also check to make sure the file to merge is correctly identifying cells of interest.

Dimensionality Reduction

• “Numerical error: classes not separable.”

Not all populations will be separable by linear discriminate analyses. Try using an alternate gene set to investigate differences between populations of interest.

Graph Window

• “Parameter not found.”

The parameter chosen is not available with your data matrix. This could indicate a serious issue with the GeqZip analysis, if available try reverting to a previous save, and check whether the parameter is available there.

• “Unknown exception during query execution.”

SeqGeq is failing to locate a dependency. Try saving your GeqZip to a new file, restart the software and try again.

Feel free to contact support with further questions: seqgeq@flowjo.com