## User: Jake Wagner

Jake Wagner130
Reputation:
130
Status:
Trusted
Location:
Last seen:
5 days, 1 hour ago
Joined:
9 months, 3 weeks ago
Email:
j*******@fredhutch.org

#### Posts by Jake Wagner

<prev • 18 results • page 1 of 2 • next >
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... Your workspace was produced by FlowJo version 7.6.5, which handled Logicle transformations significantly differently. I took your workspace and loaded it in to FlowJo version 10.6.1, which itself raised a dialog box to emphasize the changes since the old version: "This workspace has one or more ...
written 6 weeks ago by Jake Wagner130
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... It's a little hard to say without seeing the workspace. Would you be able to provide me with the workspace file somehow? Email would be fine: jpwagner@fredhutch.org. It seems strange that it would error out at Log FL 4 (rather than right away at Log FL 1) which makes me think there is something ...
written 10 weeks ago by Jake Wagner130
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... Sorry for the delay. Glad to hear you figured it out. Go ahead and try both approaches and let me know how it works out. :-) ...
written 4 months ago by Jake Wagner130
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... I'll gladly look in to your function quickly to see what the issue might be, but have you also checked out tailgate (it will be renamed gate_tail in the upcoming API changeover). It uses the derivative of the KDE to handle this situation (one peak, so no valley). One of the vignettes briefly tou ...
written 4 months ago by Jake Wagner130
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... Hi @riedel. As the error message says, the matrix you are trying to use for compensation is not invertible (in other words, it's "singular"). The compensation calculation requires that the matrix be invertible, so the compensate method is appropriately failing. In this case, starting with a zero ...
written 4 months ago by Jake Wagner130
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... You can do this using a transformList, which is discussed a bit in the package vignette. Additionally, logicleTransform() will give you default transformation parameters, but you should look at estimateLogicle() to estimate these for your data. Anyway, try this (adapted from your code):  # ...
written 5 months ago by Jake Wagner130
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... Well, this was a bit before my arrival on the team for flowCore, but I think most of the answers to your questions can be found in this commit: https://github.com/RGLab/flowCore/commit/30d9fc3fd7e46f9b75a45c6410b4a9c43233a8d8 The original C implementation of biexponential_transform is there, a ...
written 5 months ago by Jake Wagner130
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... No problem. Thanks for including the files and code. It makes troubleshooting so much easier. ...
written 6 months ago by Jake Wagner130
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... Do you just want the matrix of the measured intensities? If so then the exprs method will extract that slot. So, if fr is your flowframe, exprs(fr). ...
written 6 months ago by Jake Wagner130
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... There are a few different issues at play here. First, your error is coming about from a simple typo. The argument to specify the forward scatter parameter is fsc, not fcs`. Second, you can only specify a single column name for each scatter parameter, not a vector of names. That is, you have this: ...
written 6 months ago by Jake Wagner130

#### Latest awards to Jake Wagner

Scholar 9 months ago, created an answer that has been accepted. For A: flowCore filterSummary toTable() function not working
Scholar 9 months ago, created an answer that has been accepted. For A: how to use the flowCore spillover function
Scholar 9 months ago, created an answer that has been accepted. For A: Convert Flowframe to matrix
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: FCSTransTransform() implementation in flowCore

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