Measure Median Fluorescence Intensity in openCyto
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justinyi10 ▴ 10
@justinyi10-13409
Last seen 4.2 years ago

I am using openCyto to gate CD markers, but instead of returning counts (using getPopStats function) I was wondering if there is a way to return the Median Fluorescence Intensity (MFI) for each sample in my gating set.

opencyto • 1.1k views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 12 days ago

You can use cytoUtils

devtools::install_github("RGLab/cytoUtils")

getStats(gs, nodes, type = pop.MFI)
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cytoUtils is dependent on RProtoBufLib but RProtoBufLib is not available for R 3.4.1. Therefore I am unable to install cytoUtils, as I am hit with an error (see below). What should I do?

ERROR: dependency ‘RProtoBufLib’ is not available for package ‘cytoUtils’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/cytoUtils’
Installation failed: Command failed (1)

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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 12 days ago

install RProtoBufLib from github the same way

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I get a 404 Not Found error when using the command shown below. I notice that the url is (https://api.github.com/repos/RGLab/RProtoBufLib/zipball/master). Is there a way to change the url so that the branch is 'trunk' and not 'master'

devtools::install_github("RGLab/RProtoBufLib")

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typing ?install_github