flowjo_to_gatingset(), colname not found: error

[KammannT]

Hi, I am struggling to parse a flowjo.wsp file containing all the compensation and gating for my fcs files.

library(CytoML) fcs_dir <- 'PathtoFolderoffcsfiles' wsp_file <- 'PathtoFlowjowspfile' flow <- CytoML::open_flowjo_xml(wsp_file)

The workspace can be loaded and indicates number of samples, groups, keywords, etc.

test <-CytoML::flow_to_gatingset(flow, path=fcs_dir, name=1)

line above gives the error: "Error in (function (ws, group_id, subset, execute, path, cytoset, backend_dir, : colname not found: Comp-BV605-CD161"

Loading a .xml file of the same Flowjo workspace (instead of .wsp) gives a different error but can however save the file:

xml_file <- 'PathtoFlowjoxmlfile' flow2 <- CytoML::open_flowjo_xml(xml_file)

Error message: ^namespace error: Namespace prefix data-type on fas-dimension is not defined <data-type:fcs-dimension data-type:name="Comp-BUV737-CD69"^

test2 <-CytoML::flow_to_gatingset(flow2, path=fcs_dir, name=1)

line above gives the error: Error in (function (ws, group_id, subset, execute, path, cytoset, backend_dir, : *: unknown tranformation type!transforms:linear

Support is very much appreciated! Thanks

[mikejiang]

What if you choose second group?i.e. name=2

[KammannT]

What if you choose second group?i.e. name=2

Gives exactly the same error: _"Error in (function (ws, group_id, subset, execute, path, cytoset, backenddir, : colname not found: Comp-BV605-CD161"