Error in SPADE.driver - specifically the unused DOWNSAMPLED_EVENTS

[alexg636]

Hello,

I've already subposted this in a past thread, but in trying out CytoSpade for the first time, I've stumbled upon the error:

Error in SPADE.driver(FILE_TO_PROCESS, file_pattern = "*.fcs", out_dir = OUTPUT_DIR, : unused argument (downsampling_samples = DOWNSAMPLED_EVENTS) Execution halted

In hopes of solving it, I've gone into the runSPADE.R file and changed it such that: DOWNSAMPLED_EVENTS = NULL

After going back into CytoSpade to "Run SPADE", it appears the runSPADE.R file gets updated (even without my generating a new runSPADE script); this essentially undos my earlier substitution and I am presented with the same error.

Is there a step I may be missing, or is there anything else I can do to alleviate the problem?

Thanks!

*Old thread: https://github.com/nolanlab/spade/issues/95

[zbjornson]

We have someone working on this issue. Thanks for being patient! In the meantime, a 30 day trial of the version of SPADE in Cytobank is available at https://dvs.cytobank.org/cytobank/.

[nsrilaxmi]

Hello, I am also getting the same error. Would you please update me if there is any solution for the below issue: SPADE.driver(FILE_TO_PROCESS, filepattern=".fcs", out_dir=OUTPUT_DIR, cluster_cols=CLUSTERING_MARKERS, panels=PANELS, transforms=TRANSFORMS, layout=LAYOUT_FUNCTION, downsampling_samples=DOWNSAMPLED_EVENTS, downsampling_target_pctile=DOWNSAMPLING_TARGET_PCTILE, downsampling_exclude_pctile=DOWNSAMPLING_EXCLUDE_PCTILE, k=TARGET_CLUSTERS, clustering_samples=CLUSTERING_SAMPLES) Error in SPADE.driver(FILE_TO_PROCESS, filepattern = ".fcs", out_dir = OUTPUT_DIR, : unused argument (downsampling_samples = DOWNSAMPLED_EVENTS) Execution halted

Thanks, Sri

[zbjornson]

This has been fixed in the cytoscape-3 branch and will be released shortly.

[zbjornson]

Duplicates #95