User: Jake Wagner

gravatar for Jake Wagner
Jake Wagner130
Reputation:
130
Status:
Trusted
Location:
Last seen:
3 days, 13 hours ago
Joined:
7 months, 2 weeks ago
Email:
j*******@fredhutch.org

Posts by Jake Wagner

<prev • 17 results • page 1 of 2 • next >
1
vote
0
answers
55
views
0
answers
Comment: C: Problem parsing data with parseWorkspace
... 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 Wagner130
0
votes
2
answers
134
views
2
answers
Comment: C: custom gatingMethod not functioning / registering as expected (openCyto) (minDen
... 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 Wagner130
1
vote
2
answers
134
views
2
answers
Answer: A: custom gatingMethod not functioning / registering as expected (openCyto) (minDen
... 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 Wagner130
1
vote
2
answers
110
views
2
answers
Answer: A: flowCore issue: creating and applying new compensation matrix
... 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 Wagner130
0
votes
1
answer
81
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 3 months ago by Jake Wagner130
3
votes
1
answer
148
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 3 months ago by Jake Wagner130
0
votes
1
answer
140
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 3 months ago by Jake Wagner130
1
vote
1
answer
114
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 3 months ago by Jake Wagner130
2
votes
1
answer
140
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 4 months ago by Jake Wagner130
0
votes
1
answer
143
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 4 months ago by Jake Wagner130

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
Scholar 7 months ago, created an answer that has been accepted. For A: Convert Flowframe to matrix
Teacher 7 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: 247 users visited in the last hour