User: Andrew Box

gravatar for Andrew Box
Andrew Box10
Reputation:
10
Status:
New User
Location:
Kansas City, MO - Stowers Institute for Medical Research
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 8 months ago
Email:
a**@stowers.org

Posts by Andrew Box

<prev • 14 results • page 1 of 2 • next >
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Comment: C: gatingML examples needed
... Thanks Mike! I'll try it. ...
written 6 weeks ago by Andrew Box10
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gatingML examples needed
... I'm struggling to work with some published example data that has a companion gatingML file. I want to begin by viewing and plotting all the gates in the analysis schema, ideally with some illustration of the hierarchies. It's the Nilsson_rare dataset [from this flowrepository?][1] Suggestions f ...
flowcore flowutils gatingml written 6 weeks ago by Andrew Box10 • updated 6 weeks ago by Jiang, Mike1.2k
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Comment: C: Opencyto - detector name not found in flow data, but pretty sure it's there
... Thanks, I ended up taking a different path for this project besides using flowWorkspace since it was giving me trouble, but I'll try and find some time to revisit this issue and confirm whether this name mismatch was in fact the issue. ...
written 6 months ago by Andrew Box10
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Comment: C: can't make clusters with SNOW package
... Ah, yes I see.  I need to either specify SOCK as the type or use makeSOCKcluster().  Maybe the previous version the default was SOCK?  I know I'm using the same code, at least this line, as what was running a while back.  I did get into 'package he#*' a while ago and had to re-install a few things, ...
written 11 months ago by Andrew Box10
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can't make clusters with SNOW package
... This was working a couple weeks ago, it's not clear what may changed in my environment.  Restarting my session and reinstalling snow and rmpi hasn't resolved.  Anyone seen this or have an idea what's going on?   > cl <- makeCluster(numcores) #make that many nodes Loading required namespace: ...
snow parallel computation written 11 months ago by Andrew Box10
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Comment: C: trouble showing a polygon gate using geom_gate
... Oh my, yes that's all it is.  I was thinking even if an edge was off scale the left-hand vertical line of the polygon would still be drawn and visible, but apparently that's not the case.  The range of the data is slightly less that the ranges of some of the polygon vertices.  Forcing xlim and ylim ...
written 12 months ago by Andrew Box10
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Answer: A: trouble showing a polygon gate using geom_gate
... deleted - 20 characters ...
written 12 months ago by Andrew Box10
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Comment: C: flowCore estimate logicle - error in getChannelMarker
... Thanks for the reply and explanation - this makes sense. And sorry for the late response, I wasn't getting notifications for some reason.  From inspecting the getChannelMarker function, it seems matching uses fix = TRUE in the current version of flowCore.  Which explains why I am no longer encounter ...
written 12 months ago by Andrew Box10
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trouble showing a polygon gate using geom_gate
... I'm having success using ggcyto and the geom_gate function to show rectangle gates.  However, when I follow the same approach to show a polygon gate, I get a warning message that I don't understand.  The hex plot is made, but no gate lines are plotted.  Are more arguments to geom_gate required when ...
flowcore ggcyto written 12 months ago by Andrew Box10 • updated 12 months ago by Jiang, Mike1.2k
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flowCore estimate logicle - error in getChannelMarker
... Hi, I'm trying to use an approach I've used in the past to transform parameters in flowCore, but I get an error after running estimateLogicle that states Error in getChannelMarker(x, channel) : can't find *593/40 [YG] I get this message whether I specify one or several channels to transform, I've ...
flowcore flow cytometry transformation written 16 months ago by Andrew Box10 • updated 16 months ago by SamGG180

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