User: Jake Wagner
Jake Wagner • 130
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Posts by Jake Wagner
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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 11 days ago by
Jake Wagner • 130
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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 9 weeks ago by
Jake Wagner • 130
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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 9 weeks ago by
Jake Wagner • 130
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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 11 weeks ago by
Jake Wagner • 130
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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 3 months ago by
Jake Wagner • 130
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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 3 months ago by
Jake Wagner • 130
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... No problem. Thanks for including the files and code. It makes troubleshooting so much easier. ...
written 3 months ago by
Jake Wagner • 130
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Answer:
A: Convert Flowframe to matrix
... 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 3 months ago by
Jake Wagner • 130
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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 4 months ago by
Jake Wagner • 130
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... After a few recent commits linked at the issue above, the `rrcov` dependency (among others) is removed from `flowCore` and those changes will be incorporated in to the next Bioconductor release. ...
written 4 months ago by
Jake Wagner • 130
Latest awards to Jake Wagner
Scholar
7 months ago,
created an answer that has been accepted.
For A: flowCore filterSummary toTable() function not working
Scholar
7 months ago,
created an answer that has been accepted.
For A: how to use the flowCore spillover function
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: FCSTransTransform() implementation in flowCore
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