Comments (2)
rohitfarmer
commented on July 29, 2024
I figured out this issue. I had to downgrade Bioconductor to 3.13 for the CytoML, flowWorkspace, and flowcore to work. However, now I have a different issue. The exported cells do not match the original data either in the timestamp or the channel values. Somehow, the data is being transformed.
I tried to switch off any transform flag in my functions. However, it is still the same.
gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(data_folder, "all-fcs-files"), execute = TRUE, transform = FALSE)
getdat <- gs_pop_get_data(gs, y = g, inverse.transform = FALSE)Any suggestions would be helpful. Thanks!
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mikejiang
commented on July 29, 2024
See here RGLab/flowWorkspace#381 (comment)
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Related Issues (20)
- try(eval(substitute(subset)), silent = TRUE) in flowjo_to_gatingset causes error when the subset argument is passed by lapply HOT 1
- CytoML Xml File Parsing Issues HOT 8
- Issue Parsing FlowJo (v10.7.2) XML File HOT 3
- FCS Express compatibility HOT 7
- Get indices of gated events from a FJ workspace / alternative to flowjo_to_gatingset HOT 5
- gs-to-flowjo Singularity issue HOT 2
- Ellipses coordinates are not correct in Gating Set after flowJo workspace parsing - v2.9.0 HOT 4
- R Session Aborts when calling flowjo_to_gatingset() more than once HOT 3
- gatingset_to_flowjo() fails with unsupported transformation: LIN
- Using FlowJo gating on pre-compensated, pre-transformed FCS files HOT 5
- flowjo_to_gatingset troubleshoot: "unknown tranformation type!transforms:linear" HOT 3
- flowjo_to_gatingset(), colname not found: error HOT 2
- extract inverse transform
- flowjo_to_gatingset does not accept data.frame as path HOT 5
- flowCore::read.FCS works but CytoML::flowjo_to_gatingset fails; no valid FCS file HOT 11
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