Comments (11)
Thanks for your input I think I figured it out:
It may have been a malformatted special character in the $FIL-Keyword. Some system along the way must have turned an Ü into something different. When I changed the $FIL-Keyword without extraordinary characters it worked.
While additional keywords can be added to identify FCS files by flowjo_to_gatingset(), the $FIL keyword appears to be obligatory.
I thought I tried to fix the issue that way earlier but it did not help then. When I tried again it did help.
Sorry for disturbing you.
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Here you can find a respective FCS file (https://www.dropbox.com/s/t3qaixahp6vze78/test.fcs?dl=0).
As described, flowCore::read.FCS works. But when the file is within a flowjo workspace and one tries to read the workspace with CytoML::flowjo_to_gatingset the above mentioned error comes up. Any ideas?
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I am also having a hard time to find out where this is triggered. I think it is somewhere in the C++ routine which I am not familiar with. I wonder what exactly makes the function think this is not a valid FCS file.
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What happens if you pass emptyValue = F
to CytoML::flowjo_to_gatingset
instead when reading the file?
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Same error.
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Incidentally, a colleague was facing a similar error using read.flowSet(path = "somedir"). In fact, there was a non FCS hidden file in the dir, which leads to the same error. As read.flowset does not show the file being invalid, it tooks me a few minutes before finding it, as all FCS files were correctly read with read.FCS. Maybe the same problem...
Best,
Samuel
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I tried to trace the error. So I isolated a respective FCS file and the related workspace. Hence I would say this is unlikely. Thanks for your input though.
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Your OS is MacOS, Linux or Windows?
from cytoml.
MacOS
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I cannot test this OS.
I don't see why the FCS could be invalid. The raised error depends only checking the first bytes of the file. So very strange.
I would apply list.files()
to the directory that contains the FCS files. I think this the same directory as the workspace file. It might be surprising.
What you could try is to add one of the following arguments to https://rdrr.io/bioc/CytoML/man/flowjo_to_gatingset.html()
:
- specify the
fcs_extension
to be "\.fcs$" in case it is currently not strict enough - use
subset
to specify explicitly the FCS files to load (IIUC)
Hope this help.
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That's OK to try helping as long as the helpers get some feedback in the end. It's good to keep a track in order to help if the case occurs again.
Your feedback really shows that only basic characters should be used from the very beginning, ie the acquisition.
Thanks for your contribution.
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Related Issues (20)
- 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
- Export populations as dataframe from a FlowJo workspace HOT 2
- extract inverse transform
- flowjo_to_gatingset does not accept data.frame as path HOT 5
- boolean gate error
- Incompatible with Apple Silicon Mac HOT 7
- flowjo_to_gatingset ignore range as defined in FCS files HOT 3
- Support for FCS 3.2? HOT 4
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