Closed anaraserikbek closed 7 years ago
A1: I will put up a vignette for that as promised
A2: with ggcyto
package, you are able to switch from parent
to gate
name by strip.text
argument,
see details in ?autoplot.GatingHierarchy
A3: there is type
argument for geom_stats
layer, see ?geom_stats
A4: You should loop through flowSet
and compensate each individual flowFrame
. e.g.
fs_comp <- fsApply(fs, function(fr){
comp <- spillover(fr)[["$SPILLOVER"]] #could be SPILL
compensate(fr, comp)
})
A5: bioc
is stable version, git
is considered to be bleeding edge (although bioc devel
branch is pretty much synced with git trunk
once a week
A6: gate_range
should be as vague/large as possible so that it is applicable across different data sets. The main purpose for this parameter is to prevent the algorithm from being interfered by some extreme outlier signals
A7-8: Cytokine
gate is deprecated by tailgate
, See ?tailgate
for the details of its parameters
A9: As long as these FCS files can be loaded with flowCore
through read.FCS
, they should be ready to use in openCyto
A10: pop
column doesn't look at the actual population name
, it is the alias
column that defines the name, so you can simply put A+/-B+/-
in pop
column
A11: Here are two workshops done by @gfinak in the past https://github.com/gfinak/BioC2015OpenCyto https://www.bioconductor.org/help/course-materials/2014/BioC2014/OpenCytoPracticalComponent.html
Thank you a lot Mike! Especially for Q10, it's working now
Thank you in advance ! as I was saying earlier if it's too much to type, we can always call if it'd be faster/more convenient for the package developers. also, I can create a separate issue#/issue for each question, if you'd consider it more appropriate.