User: Ulrik Stervbo

gravatar for Ulrik Stervbo
Reputation:
30
Status:
New User
Location:
Germany
Twitter:
ulrikstervbo
Last seen:
1 year, 6 months ago
Joined:
11 years, 6 months ago
Email:
u************@gmail.com

Posts by Ulrik Stervbo

<prev • 14 results • page 1 of 2 • next >
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Comment: C: OpenCyto -- proper gating of CD45
... I am using flowclust.2d to identify granulocytes, but it always sems the gate is either too narrow and excludes too many immature and eosinophils, or becomes far too long and includes - depending on sample - to many lymphocytes. flowClust.2d: quantile=0.83, K = 2, target = c(5,600), with the prior_ ...
written 19 months ago by Ulrik Stervbo30
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OpenCyto -- time gate and border events
... Hello everyone, does anyone know if and how I can remove border events in all channels without specifying each channel in the template? Also, I would like to have a time gate, is this possible? I know i can do both with flowcore, but I also like the idea of a readable template, and would hate to m ...
flowcore opencyto gating flow cytometry written 19 months ago by Ulrik Stervbo30 • updated 19 months ago by Jiang, Mike1.0k
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OpenCyto -- proper gating of CD45
... Hello, I am trying to analyse monocytes, lymphocytes and granulocytes by CD45/SSC. I am not sure how to do the gating with openCyto. Attached is an immage of how I'd do it by hand, and what I can get so far with open cyto. Some cells are not lysed and must be removed - they are low in CD45 and sid ...
flowworkspace opencyto gating written 19 months ago by Ulrik Stervbo30 • updated 19 months ago by Jiang, Mike1.0k
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Answer: A: OpenCyto - getting gate coordinates
... I just came across getGate(). Extraction of values depend on the gate but could be the way forward ...
written 19 months ago by Ulrik Stervbo30
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Comment: C: OpenCyto - getting gate coordinates
... True that strange proportions are indication of strange gates (I am also using at the CV as you do in https://www.bioconductor.org/help/course-materials/2015/BioC2015/OpenCytoWorkshop.html) but I also need to adjust strange gates that might not give rise to strong outliers. We still inspect the samp ...
written 19 months ago by Ulrik Stervbo30
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OpenCyto - getting gate coordinates
... I would like to be able to identify samples where the gating applied with opencyto is odd. Instead of inspecting each sample, I am thinking of plotting the gate coordinates. Is this possible? Thanks in advance. Ulrik ...
opencyto written 19 months ago by Ulrik Stervbo30
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OpenCyto - getting the gates correct
... Hello Everyone, I am trying to construct a GatingSet and apply it to a few samples. I have difficulties getting the gates to end where they should. In particular I often find the CD8+ gate being utterly wrong (see the attached bitmap). Is there any way I can modify things so the gates end up in a m ...
opencyto gating written 19 months ago by Ulrik Stervbo30
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Comment: C: openCyto - flowclust.2d throws errors
... > sessionInfo() R version 3.2.5 (2016-04-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.10 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 LC_MONETARY=de_DE.UTF-8 [6] LC_MESSAGES=de_DE.UTF-8 LC_ ...
written 19 months ago by Ulrik Stervbo30
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openCyto - flowclust.2d throws errors
... Hello everyone, I have problems getting the flowClust.2d to work. library(flowViz) library(openCyto) data(GvHD) fr <- GvHD[[2]] trs <- logTransform() fr_trans <- transform(fr, `FL1-H` = trs(`FL1-H`), `FL2-H` = trs(`FL2-H`)) fr_trans fres <- flowClust.2d(fr = fr_trans, xChannel = "F ...
opencyto flow cytometry written 19 months ago by Ulrik Stervbo30 • updated 18 months ago by bmuchmore0
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flowDensity, nmRemove and xyplot
... Hello everyone, I am trying to remove margin events in my flow data and came across flowDensity. After removing margin events plotting with xyplots fails. Is this known behaviour? 'boundaryFilter' from flowCore works without problems. Best, Ulrik ​library(flowDensity) library(flowViz) # Exam ...
flowviz flowdensity written 20 months ago by Ulrik Stervbo30 • updated 20 months ago by Jiang, Mike1.0k

Latest awards to Ulrik Stervbo

Popular Question 19 months ago, created a question with more than 1,000 views. For Problem with HDF5 and ncdfFlow
Scholar 2.2 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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