User: Andrew Box

gravatar for Andrew Box
Andrew Box0
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Location:
Kansas City, MO - Stowers Institute for Medical Research
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1 month, 2 weeks ago
Joined:
11 months, 1 week ago
Email:
a**@stowers.org

Posts by Andrew Box

<prev • 11 results • page 1 of 2 • next >
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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 9 weeks ago by Andrew Box0
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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 9 weeks ago by Andrew Box0
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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 3 months ago by Andrew Box0
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Answer: A: trouble showing a polygon gate using geom_gate
... deleted - 20 characters ...
written 3 months ago by Andrew Box0
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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 3 months ago by Andrew Box0
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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 3 months ago by Andrew Box0 • updated 3 months ago by Jiang, Mike1.1k
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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 7 months ago by Andrew Box0 • updated 7 months ago by SamGG150
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Answer: A: get vertex xy coords from igraph mst plot
... layout <- layout_with_fr(mymst, dim = 2, niter = 500) This is what I was looking for.  Part of the mistake I was making was running the layout on my original graph object 'g', not the mst graph object 'mymst'.   Layout now contains the x and y coordinates for the vertices of the minimum spannin ...
written 8 months ago by Andrew Box0
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get vertex xy coords from igraph mst plot
... I'm interested in getting the X and Y coordinates from a minimum spanning tree to use for some non-igraph plotting and export for merging with another data set.  However, I'm having trouble understanding how to obtain the coordinates from the graph object.  It seems that typically, the layout would ...
igraph written 8 months ago by Andrew Box0
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Opencyto - detector name not found in flow data, but pretty sure it's there
... Hi, I've saved a wsp workspace in flowjo X that I'm attempting to import into R using opencyto using this code below.  The files are from a ZE5 analyzer. flowDataPath <- getwd() wsfile <- list.files(flowDataPath, pattern="FJ.wsp",full = TRUE) ws <- openWorkspace(wsfile) gs <- parseWorks ...
flowcore opencyto flow cytometry written 9 months ago by Andrew Box0 • updated 7 months ago by jd8410290

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