User: Jake Wagner

gravatar for 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 >
0
votes
1
answer
46
views
1
answers
Answer: A: Issue creating transformed filter in flowCore
... 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
3
votes
1
answer
88
views
1
answers
Answer: A: FCSTransTransform() implementation in flowCore
... 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
0
votes
1
answer
73
views
1
answers
Comment: C: how to use the flowCore spillover function
... No problem. Thanks for including the files and code. It makes troubleshooting so much easier. ...
written 5 weeks ago by Jake Wagner100
1
vote
1
answer
60
views
1
answers
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 Wagner100
2
votes
1
answer
73
views
1
answers
Answer: A: how to use the flowCore spillover function
... 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
0
votes
1
answer
98
views
1
answers
Comment: C: flowCore install missing a dependency?
... 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
1
vote
1
answer
98
views
1
answers
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 8 weeks ago by Jake Wagner100
0
votes
2
answers
116
views
2
answers
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 9 weeks ago by Jake Wagner100
1
vote
2
answers
116
views
2
answers
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 10 weeks ago by Jake Wagner100
0
votes
2
answers
116
views
2
answers
Comment: C: Cannot inverse transform GatingSet
... 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 382 users visited in the last hour