User: peterfoster

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peterfoster20
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3 years, 9 months ago
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Posts by peterfoster

<prev • 6 results • page 1 of 1 • next >
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Inconsistent Subseting using norm2Filter in FlowCore
... I recently discovered that the application of (at least) `norm2Filter()` is not consistent when replicated.  I've pasted an example below.  In the example dataset the differences are small--just a few events.  In my much larger experimental datasets, however, the number of events changes by the hund ...
flowcore filter subsetting gate written 3.8 years ago by peterfoster20 • updated 3.8 years ago by Jiang, Mike1.2k
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Comment: C: assign the y-scale relation in flowViz densityplot
... Thank you for your example, I did try it and play with it in an attempt to achieve my aims... As a density plot (i.e. histogram) the y-axis to which I refer is the event count at each value of x.  Yes, your example rescales the x axis, but leaves the y axis of each trace untouched, having a default ...
written 4.3 years ago by peterfoster20
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Comment: C: assign the y-scale relation in flowViz densityplot
... Seeing your syntax for this was informative for me, but ultimately this did not change the way the y-axis (or x, as you had typed) is plotted for each dataset in the flowframe.  This appears to affect how the plot window for the two channels are treated, not the y-scale for the individual traces wit ...
written 4.3 years ago by peterfoster20
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assign the y-scale relation in flowViz densityplot
... I'm using the densityplot function in flowViz to plot various channels of a flowSet. densityplot(~., fs.gated.1, channels=c("deflog.V1", "deflog.Y2"), margin=FALSE, col="black") How can I set the y-scale to be the same across all of the samples/flowframes?  ylim sets the entire plot ...
flowviz densityplot written 4.3 years ago by peterfoster20 • updated 3.6 years ago by magomudw0
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Comment: C: How are autofluorescence values used in the spillover/compensate functions?
... Thank you for your help!   That being the case, I'm confused as to why the mean/median for my unstained controls is practically the same in both the uncompensated and compensated data.  If the blank mean/median is rolled into the compensation matrix, compensation should transform the mean/median to ...
written 4.3 years ago by peterfoster20
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How are autofluorescence values used in the spillover/compensate functions?
... Could someone provide a more detailed explanation as to how autoflourescence values are handled in the spillover and compensation functions in the flowCore package?  I can't figure out how to view the function's code...   I know that the autoflourescence/baseline data can be specified in the spillo ...
flowcore flow cytometry compensation spillover written 4.3 years ago by peterfoster20 • updated 4.3 years ago by Greg Finak150

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