## User: Jake Wagner

Jake Wagner100
Reputation:
100
Status:
Trusted
Location:
Last seen:
4 days, 23 hours ago
Joined:
4 months, 3 weeks ago
Email:
j*******@fredhutch.org

#### Posts by Jake Wagner

<prev • 13 results • page 1 of 2 • next >
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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 Wagner100
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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 Wagner100
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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 Wagner100
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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 5 weeks ago by Jake Wagner100
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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 Wagner100
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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 Wagner100
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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 Wagner100
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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 Wagner100
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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 Wagner100
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... Moved comment to answer ...
written 10 weeks ago by Jake Wagner100

#### 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
Scholar 4 months ago, created an answer that has been accepted. For A: Convert Flowframe to matrix
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: FCSTransTransform() implementation in flowCore

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