User: Rivka

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Rivka0
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Posts by Rivka

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Comment: C: Trouble adapting openCyto Transformation
... our template sucked, thats why it wasn't working ...
written 2.5 years ago by Rivka0
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Use "gating.template" on data.table
... Hello, I am working on a small app that allows the user to create a gating Template on html based textInput which is stored in an 'R' data.table(including all the needed columns). I would now like to use the opencyto's  gating.Template function to use the Users Input for  automated gating without h ...
opencyto gating R csv files data.table written 2.5 years ago by Rivka0
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Comment: C: openCyto trouble importing xml file
... Hello, sorry I did not see your comment earlier due to our new baby:-) What I changed: I did not use the actual xml file but just the workspace,that you can download from flowjo, and has the suffix .wsp and that worked for me. See picture more more information:  https://goo.gl/photos/KcK9CDTAvfkTq ...
written 2.5 years ago by Rivka0
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(Closed) Trouble adapting openCyto Transformation
... Hello, being still pretty new to OpenCyto I have been working through the bioconductor Tutorial and am now trying to reproduce the data output and plots with our data. I get an error trying to do the transformation part: ###################### # Transformation chnls <- parameters(m_compMat) tra ...
opencyto gating written 2.8 years ago by Rivka0
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openCyto displaying gating panels
... Hello, when displaying my gating panels with plotGate(gh), I get all panels in one window, as I like it.  I now need to customize the axises for some of the panels separately but cannot find a function to still have all panels showing in one window in a 4*4 arrangement. The following shows them in ...
opencyto written 2.9 years ago by Rivka0 • updated 2.9 years ago by Jiang, Mike1.2k
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openCyto working Example: expects {flowWorkspace} but example
... Hello, I've been working with http://isac-net.org/PDFS/c2/c281b4c1-b834-4347-abe5-faa807dd5647.pdf in order to use it for my own data later on. I have trouble with this part: #Annotation keyword_vars<-c("$FIL","Stim","Sample Order","EXPERIMENT NAME") #relevant keywords pd<-data.table(getK ...
opencyto opencyto gating bioconductor written 2.9 years ago by Rivka0 • updated 2.9 years ago by Jiang, Mike1.2k
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Answer: A: Parsing flowWorkspace data
... 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 ...
written 3.0 years ago by Rivka0
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Parsing flowWorkspace data
... 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 F ...
flowworkspace opencyto R bioconductor written 3.0 years ago by Rivka0 • updated 2.9 years ago by Jiang, Mike1.2k
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Answer: A: openCyto trouble importing xml file
... Hey, it was a problem of the xml-file itself. I fixed it and now it's working. ...
written 3.0 years ago by Rivka0
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openCyto trouble importing xml file
... Hello, I am very new to openCyto and trying to  import a xml file (being a workspace from FlowJo.) I keep getting an error saying  "Error in xpathApply(x, "/Workspace", function(x) xmlGetAttr(x, "version"))[[1]] : Indexing beyond border # Open workspace wsfile<-"flowjo_ws.xml" ws<-openWorks ...
opencyto R bioconductor written 3.0 years ago by Rivka0

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