Parsing flowWorkspace data
2
0
Entering edit mode
Rivka • 0
@rivka-11959
Last seen 4.3 years ago
Munich

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

 

 

 

opencyto R flowworkspace bioconductor • 680 views
ADD COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode
Rivka • 0
@rivka-11959
Last seen 4.3 years ago
Munich

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 COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 12 days ago
(Private Address)

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

ADD COMMENT

Login before adding your answer.

Traffic: 140 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6