Hello,
when parsing my flowjo workspace and fcs file(for testing) as described in the tutorial,
gs <- parseWorkspace(ws, name= "All Samples", path = "data/FCS", isNcdf = TRUE)
I get an error: "the logical operators and the gating paths do not pair correctly! "
Unfortunately am very new to FlowCytometry and so far cannot find out what my data problem is, what I need to look for and change.
Thanks, Rivka
Thanks!
still, I am not quite sure, what I need to look for in my output.
it tells me:
parse the population Node:CD107+IFNg+IL2+Mip1b+TNF+
free gate:TNF-
free gate:Mip1b-
free gate:IL2-
free gate:IFNg-
free gate:CD107-
free gate:TNF
free gate:Mip1b
free gate:IL2
free gate:IFNg
free gate:CD107
free gate:CD4
free gate:CD3
free gate:Single Cells
free gate:Lymphocytes
Fehler: the logical operators and the gating paths do not pair correctly!
I do find the node in the xml file, what what exactly do I need to look for?
here is the (I hope) xml-file part:
<AndNode name="CD107+IFNg+IL2+Mip1b+TNF+" annotation="" owningGroup="" expanded="0" sortPriority="15" count="2" >
<Graph smoothing="0" backColor="#ffffff" foreColor="#000000" type="Pseudocolor" fast="1" >
<Axis dimension="x" name="Comp-V450-A" label="" auto="auto" />
<Axis dimension="y" name="Comp-PerCP-Cy5-5-A" label="" auto="auto" />
<GraphSettings level="5%" smoothingHighResolution="1" contourHighResolution="1" histogramSmoothingCount="0" graphResolution="256" showOutliers="0" drawLargeDots="0" dotsToDraw="8000" tint="le.chartfill.tinted.40" lineWeight="le.lineweight.normal" lineStyle="le.linestyle.solid" />
<GraphEnvironment showGrid="0" showAxes="tnlTNL" showGates="1" showFreqOnPlots="1" showGateNameOnPlots="1" showMedians="0" showUncomped="0" addEventParam="0" lastYAxisName="" >
<TextTraits font="SansSerif" size="11" name="Labels" style="plain" color="#000000" background="#00ffffff" just="left" />
<TextTraits font="SansSerif" size="11" name="LayoutGates" style="plain" color="#000000" background="#00ffffff" just="left" />
<TextTraits font="SansSerif" size="9" name="Numbers" style="plain" color="#000000" background="#00ffffff" just="left" />
<TextTraits font="SansSerif" size="9" name="Legend" style="plain" color="#000000" background="#00ffffff" just="left" />
<WindowPosition x="697" y="45" width="450" height="553" displayed="0" panelState="---" />
</GraphEnvironment>
</Graph>
<Dependents>
<Dependent name="Lymphocytes/Single Cells/CD3/CD4/CD107" />
<Dependent name="Lymphocytes/Single Cells/CD3/CD4/IFNg" />
<Dependent name="Lymphocytes/Single Cells/CD3/CD4/IL2" />
<Dependent name="Lymphocytes/Single Cells/CD3/CD4/Mip1b" />
<Dependent name="Lymphocytes/Single Cells/CD3/CD4/TNF" />
</Dependents>
<
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version 2.3.6
It indicates the issue of the definition for some `bool gate` (i.e. `AND` `OR` gate in flowJo) in xml. To troubleshoot, you can enable the debug mode by `flowWorkspace::setLoglevel("Gate")`. It prints the details as the parser proceeds when you run `parseWorkspace`, by which you will know what exact population/gate failed. And then you can open your xml and investigate that particular node.
To turn it off, simply `flowWorkspace::setLoglevel("None")`