Question: Parsing flowWorkspace data
0
gravatar for Rivka
3.0 years ago by
Rivka0
Munich
Rivka0 wrote:

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

 

 

 

ADD COMMENTlink modified 3.0 years ago by Jiang, Mike1.2k • written 3.0 years ago by Rivka0
1

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")`

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Jiang, Mike1.2k
Answer: Parsing flowWorkspace data
0
gravatar for Rivka
3.0 years ago by
Rivka0
Munich
Rivka0 wrote:

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>
                           <
ADD COMMENTlink written 3.0 years ago by Rivka0
1

send me the xml and I will take a look at it.

ADD REPLYlink written 3.0 years ago by Jiang, Mike1.2k
Answer: Parsing flowWorkspace data
0
gravatar for Jiang, Mike
3.0 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

It is a bug. I've fixed it in flowWorkspace 3.20.2.

ADD COMMENTlink written 3.0 years ago by Jiang, Mike1.2k
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