User: Jake Wagner

gravatar for Jake Wagner
Jake Wagner40
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40
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New User
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4 days, 12 hours ago
Joined:
2 months, 4 weeks ago
Email:
j*******@fredhutch.org

Posts by Jake Wagner

<prev • 7 results • page 1 of 1 • next >
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Answer: A: flowCore install missing a dependency?
... 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 4 days ago by Jake Wagner40
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Answer: A: Cannot inverse transform GatingSet
... 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 11 days ago by Jake Wagner40
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Answer: A: Cannot inverse transform GatingSet
... 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 12 days ago by Jake Wagner40
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Comment: C: Cannot inverse transform GatingSet
... Moved comment to answer ...
written 12 days ago by Jake Wagner40
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Comment: C: flowCore filterSummary toTable() function not working
... No problem. Hervé Pagès was kind enough to move the `toTable` generic to `BiocGenerics` to remove the masking issue from `AnnotationDBI`, so in the next release this shouldn't be a problem. ...
written 11 weeks ago by Jake Wagner40
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Answer: A: flowCore filterSummary toTable() function not working
... After carefully checking your session, I can reproduce your error. So it looks like attaching `geneplotter` is attaching `annotate`, which is attaching `AnnotationDbi`, which is masking `flowCore::toTable()`. I'll look in to the clash, but for now you can just explicitly ask for `toTable` from the ` ...
written 12 weeks ago by Jake Wagner40
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Comment: C: flowCore filterSummary toTable() function not working
... Your reproducible example seems incomplete, as `curv.filter` was never defined. I assume by "code contained in the documentation for the function", you mean effectively this: dat <- read.FCS(system.file("extdata","0877408774.B08",package="flowCore")) c1f <- curv1Filter(filterId="myCur ...
written 12 weeks ago by Jake Wagner40

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