User: k.teijgeler

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Posts by k.teijgeler

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Comment: C: custom gatingMethod not functioning / registering as expected (openCyto) (minDen
... To further diagnose my peak patterns i thought of adding the following (see code below). Is there a way to get the name of the alias or other information from the gatingFile into context in the function? KDEdata <- density(x) # new KDEdatamedian <- median(x) ...
written 10 weeks ago by k.teijgeler0
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Answer: A: custom gatingMethod not functioning / registering as expected (openCyto) (minDen
... A collegue told me to put some print() calls in the function and guess what i was referring to an incorrect object. Oeps;) KDEdata <- density(x) KDEdatamedian <- median(KDEdata) # median of KDEdata instead of median of (x) ...
written 10 weeks ago by k.teijgeler0
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Comment: C: custom gatingMethod not functioning / registering as expected (openCyto) (minDen
... Thanks for the quick answer! Good idea! I use the tailgate for other nodes but it might be better to just incoorporate a tailgate when only 1 peak and no valleys are found. Great :). To test whether i could register a new plugin i did the following: - Made a copy function of mindensity called mind ...
written 10 weeks ago by k.teijgeler0
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custom gatingMethod not functioning / registering as expected (openCyto) (minDensity)
... Dear reader, I've been happily using openCyto for a while now and i really like the mindensity gatingMethod. It's very robust in panels/samples that have 2 peaks for a marker (+- 80-90% of the samples for this particular marker, figure 1) . [figure 1][1] However i've experienced some cases in w ...
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Comment: C: how to use the flowCore spillover function
... Thanks a lot for the thorough explanation and quick response Jake, and also for correcting my typo! spillover <- spillover(fcs , unstained = 17 , fsc ="FSC.A" , ssc ="SSC.A" , useNormFilt = TRUE, patt="FSC.A|SSC.A|BV|PE|Alexa|BUV|APC|FITC", method="mean") This one works for me :) ...
written 4 months ago by k.teijgeler0
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how to use the flowCore spillover function
... Hi, i have been trying to convert a gatingset to a flowJO workspace object by using the gatingset2FlowJO function from cytoML. After some experimentation i succeeded. However i noticed that only my transformation was in the flowJO workspace and not the compensation. The problem seems to be that i do ...
flowcore spillover gatingset2flowjo written 4 months ago by k.teijgeler0 • updated 4 months ago by Jake Wagner130
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Comment: C: polyFunctions gate in OpenCyto 1.20
... Hey Jiang, sorry for the delay i am just back from holiday. I just checked and it now works in 3_8. Thanks a lot for the quickfix :) ...
written 4 months ago by k.teijgeler0
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Comment: C: polyFunctions gate in OpenCyto 1.20
... I wish that was an easy option for me. I want a solution on an R shiny server i am using, so i am a 100% everyone uses the same packages and files ect. Using separate PC's has always been problematic, some people have more or less recent versions. Thats why i am currently working on a R shiny serve ...
written 4 months ago by k.teijgeler0
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Answer: A: polyFunctions gate in OpenCyto 1.20
... When using Bioconductor 3.7 with openCyto 1.20.2, it is problematic to have + and - in the aliases in combination with polyFunctions. This example does not work (for me): [Gating Template with + and -][1] alias CD4+IL2+ CD4+IL2- ...
written 5 months ago by k.teijgeler0
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Comment: C: polyFunctions gate in OpenCyto 1.20
... Thanks for looking at it, somehow that Gating Template works for me the boolGate is not giving me a problem The following does not work for me: [polyFunctions Test][1] [1]: https://uploadfiles.io/n2q6kwg1 I installed R 3.6 and just tried the Bioc release 3.9 but i am getting the same error: [180 ...
written 5 months ago by k.teijgeler0

Latest awards to k.teijgeler

Scholar 9 months ago, created an answer that has been accepted. For A: polyFunctions gate in OpenCyto 1.20

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