## User: Ulrik Stervbo

Reputation:
30
Status:
New User
Location:
Germany
ulrikstervbo
Last seen:
2 years, 8 months ago
Joined:
12 years, 8 months ago
Email:
u************@gmail.com

#### Posts by Ulrik Stervbo

<prev • 14 results • page 1 of 2 • next >
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... 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 2.7 years ago by Ulrik Stervbo30
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... 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 ...
written 2.7 years ago by Ulrik Stervbo30 • updated 2.7 years ago by Jiang, Mike1.2k
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... 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 ...
written 2.7 years ago by Ulrik Stervbo30 • updated 2.7 years ago by Jiang, Mike1.2k
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... I just came across getGate(). Extraction of values depend on the gate but could be the way forward ...
written 2.7 years ago by Ulrik Stervbo30
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... 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 2.7 years ago by Ulrik Stervbo30
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... 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 ...
written 2.7 years ago by Ulrik Stervbo30
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... 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 ...
written 2.7 years ago by Ulrik Stervbo30
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... > 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 2.7 years ago by Ulrik Stervbo30
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... 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 ...
written 2.7 years ago by Ulrik Stervbo30 • updated 2.7 years ago by bmuchmore0
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... 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 ...
written 2.9 years ago by Ulrik Stervbo30 • updated 2.9 years ago by Jiang, Mike1.2k

#### Latest awards to Ulrik Stervbo

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Problem with HDF5 and ncdfFlow
Scholar 3.4 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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