I found that when running in gene_mode, the Q-Q Plot, Scatter Plot, MA Plot, and Volcano Plot all displayed error messages about missing objects (see below). Adding more useful information will help users understand the issue, which I stumbled upon while arbitrarily meddling with settings.
Error Messages:
Scatter Plot:
ERROR: object 'sigma_sq' not found
Q-Q Plot:
ERROR: object 'b' not found
MA Plot:
ERROR: object 'mean-obs' not found
ERROR: object 'sigma_sq' not found
Volcano Plot:
ERROR: object 'b' not found
It seems like all these error messages are related to the alternate organization of the test table while in Gene Mode.
I found that when running in gene_mode, the Q-Q Plot, Scatter Plot, MA Plot, and Volcano Plot all displayed error messages about missing objects (see below). Adding more useful information will help users understand the issue, which I stumbled upon while arbitrarily meddling with settings. Error Messages: Scatter Plot:
Q-Q Plot:
MA Plot:
Volcano Plot:
It seems like all these error messages are related to the alternate organization of the test table while in Gene Mode.