Question: Measure Median Fluorescence Intensity in openCyto
0
gravatar for justinyi10
2.3 years ago by
justinyi1010
justinyi1010 wrote:

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 • 791 views
ADD COMMENTlink modified 2.3 years ago by Jiang, Mike1.2k • written 2.3 years ago by justinyi1010
Answer: Measure Median Fluorescence Intensity in openCyto
1
gravatar for Jiang, Mike
2.3 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

You can use cytoUtils

devtools::install_github("RGLab/cytoUtils")

getStats(gs, nodes, type = pop.MFI)

See https://github.com/RGLab/cytoUtils/issues/1

ADD COMMENTlink written 2.3 years ago by Jiang, Mike1.2k

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)

ADD REPLYlink written 2.3 years ago by justinyi1010
Answer: Measure Median Fluorescence Intensity in openCyto
0
gravatar for Jiang, Mike
2.3 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

install RProtoBufLib from github the same way

ADD COMMENTlink written 2.3 years ago by Jiang, Mike1.2k

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")

ADD REPLYlink written 2.3 years ago by justinyi1010

typing ?install_github

ADD REPLYlink written 2.3 years ago by Jiang, Mike1.2k
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