User: Jiang, Mike

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Jiang, Mike1.2k
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Posts by Jiang, Mike

<prev • 261 results • page 1 of 27 • next >
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Answer: A: gatingML examples needed
... Use CytoML to Import gatingML generated from Cytobank. See https://github.com/RGLab/CytoML Then visualize the gates by ggcyto ...
written 6 weeks ago by Jiang, Mike1.2k
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Comment: C: flowCore: uneven number of tokens / The last keyword is dropped.
... suppressWarnings(read.FCS("test.fcs", emptyValue=FALSE)) ...
written 6 weeks ago by Jiang, Mike1.2k
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Comment: C: How to select left hand side of mindensity2 gate
... openCyto tries to interpret pop = '-' in a generic way (i.e. set 'negate' flag to the gate) that is not limited to 1d gate but can also work the same manner for 2d gate and even non-geometrical gate (e.g. bool gate). So you will get a negated 1d gate that is open-ended at right side and 'ggcyto' is ...
written 8 weeks ago by Jiang, Mike1.2k
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Comment: C: How to select left hand side of mindensity2 gate
... flowCore&flowWorkspace provide the relative low-level of APIs to interact with the basic data structures (e.g. flowSet, Gatingset). For the auto gating, openCyto package provides more high-level interlaces and convenient wrappers (which are built upon those two packages). They operate at the di ...
written 11 weeks ago by Jiang, Mike1.2k
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Answer: A: How to select left hand side of mindensity2 gate
... I'd recommend openCyto gating functions to be used with its template-based gating framework. Instead of iterating through each sample (i.e. fsApply) of each gated population (i.e. getData) and invoking mindensity and adding gates manually, you can simply submit the gating strategy to the framework a ...
written 11 weeks ago by Jiang, Mike1.2k
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Comment: C: ncdfFlowSet with dim=3
... Glad to hear! Thanks for reporting the issue. ...
written 11 weeks ago by Jiang, Mike1.2k
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Answer: A: ncdfFlowSet with dim=3
... see the solution here https://github.com/RGLab/ncdfFlow/issues/44#issuecomment-459527469 ...
written 11 weeks ago by Jiang, Mike1.2k
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Answer: A: RefGate populations switched in OpenCyto 1.20
... I've pushed the fix. See details https://github.com/RGLab/openCyto/commit/f0c8104c32bf8242a8d4137dd4c5826e310b2492 You can either install the development version from github or wait for the updated release build 1.20.2 from BioC site(which typically takes 1 or 2 days to appear). ...
written 3 months ago by Jiang, Mike1.2k
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Answer: A: flowCore: retain raw data in the flowset after transformation
... You can do inline transformation,e.g. newFlowSet <- transform(flowset, `trans-FL2-A` = logicleT(`FL2-A`), `trans-FL3-A` = logicleT(`FL3-A`)) By the way, why do you need the original columns? ...
written 3 months ago by Jiang, Mike1.2k
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Comment: C: RefGate populations switched in OpenCyto 1.20
... I have tried to modify the population names to simulate your use case but it still works fine for me. I think you will have to provide a minimal reproducible example in order for me to troubleshoot it. ...
written 3 months ago by Jiang, Mike1.2k

Latest awards to Jiang, Mike

Scholar 7 months ago, created an answer that has been accepted. For A: openCyto displaying gating panels
Popular Question 8 months ago, created a question with more than 1,000 views. For how to read FCS3.1 files?
Scholar 22 months ago, created an answer that has been accepted. For A: trouble showing a polygon gate using geom_gate
Scholar 22 months ago, created an answer that has been accepted. For A: openCyto displaying gating panels
Scholar 22 months ago, created an answer that has been accepted. For A: OpenCyto -- time gate and border events
Popular Question 22 months ago, created a question with more than 1,000 views. For flowCore package - logicle transformation
Scholar 23 months ago, created an answer that has been accepted. For A: openCyto displaying gating panels
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Help with flowCore
Scholar 3.0 years ago, created an answer that has been accepted. For A: OpenCyto -- time gate and border events
Scholar 3.0 years ago, created an answer that has been accepted. For A: openCyto displaying gating panels
Scholar 3.0 years ago, created an answer that has been accepted. For A: How to transform cytometry data from CSV and not FCS file?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: parsing flowFrame@description in flowCore
Scholar 3.0 years ago, created an answer that has been accepted. For A: openCyto trouble importing xml file
Scholar 3.0 years ago, created an answer that has been accepted. For A: How to FlowCore
Scholar 3.0 years ago, created an answer that has been accepted. For A: ggcyto's axis_inverse_trans: Usage with GatingSet constructed in R
Scholar 3.0 years ago, created an answer that has been accepted. For A: OpenCyto - getting gate coordinates
Scholar 3.0 years ago, created an answer that has been accepted. For A: How to edit parameters and description of fcs file
Scholar 3.0 years ago, created an answer that has been accepted. For A: parsing flowFrame@description in flowCore
Scholar 3.1 years ago, created an answer that has been accepted. For A: How to transform cytometry data from CSV and not FCS file?
Scholar 3.2 years ago, created an answer that has been accepted. For A: ggcyto's axis_inverse_trans: Usage with GatingSet constructed in R
Scholar 3.4 years ago, created an answer that has been accepted. For A: How to FlowCore
Scholar 3.4 years ago, created an answer that has been accepted. For A: timeLinePlot() ylab parameter doesn't work?
Centurion 3.5 years ago, created 100 posts.
Scholar 3.8 years ago, created an answer that has been accepted. For A: timeLinePlot() ylab parameter doesn't work?
Scholar 4.1 years ago, created an answer that has been accepted. For A: timeLinePlot() ylab parameter doesn't work?

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