User: Jake Wagner
Jake Wagner • 100
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Posts by Jake Wagner
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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 17 days ago by
Jake Wagner • 100
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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 4 weeks ago by
Jake Wagner • 100
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... No problem. Thanks for including the files and code. It makes troubleshooting so much easier. ...
written 5 weeks ago by
Jake Wagner • 100
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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 5 weeks ago by
Jake Wagner • 100
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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 5 weeks ago by
Jake Wagner • 100
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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 7 weeks ago by
Jake Wagner • 100
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... Mike re-opened an issue related to this: https://github.com/RGLab/flowCore/issues/23. I'll be moving the classes and methods that necessitate these dependencies over to `flowStats` and I'll post here and to that issue when that's complete. ...
written 8 weeks ago by
Jake Wagner • 100
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... Additionally, I went ahead and added an `inverse.transform` flag to `getData` in https://github.com/RGLab/flowWorkspace/commit/0346da50b5e876ac90465a4ecdc3aa71589b7778
Those changes will be in the Bioconductor 3.10 development branch as well and will make this a bit easier:
```
fs_inverted <- get ...
written 9 weeks ago by
Jake Wagner • 100
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... Would `getTransformations()` with `inverse=TRUE` work for your case? So something along these lines:
```
fs_transformed <- getData(gs)
inv_trans <- lapply(gs, function(gh){
invs <- getTransformations(gh, inverse=TRUE)
invs <- transformList(names(invs), invs)
})
fs_inverted <- tran ...
written 10 weeks ago by
Jake Wagner • 100
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... Moved comment to answer ...
written 10 weeks ago by
Jake Wagner • 100
Latest awards to Jake Wagner
Scholar
4 months ago,
created an answer that has been accepted.
For A: flowCore filterSummary toTable() function not working
Scholar
4 months ago,
created an answer that has been accepted.
For A: how to use the flowCore spillover function
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: FCSTransTransform() implementation in flowCore
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