flowcore: z-Score normalization of flowSet (fsApply or normalize)
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BenAbflack • 0
@benabflack-8435
Last seen 6.2 years ago
Zurich/Switzerland

Hey all,

​I am trying to normalise (some chosen) expression values of all flowFrames within a flowSet. They desired output would be again a flowSet. Unfortunately my understanding of defining functions in R is not sufficient to do so.

What I have tried so far was to use fsApply (flowcore) or normalize (flowcore) functions, however I think that both were unsuccesful because I wasnt able to define the normalization function correctly. For matrices, z-Score normalization is easily possible with the scale function, but I wasnt able to translate this into a working solution for flowSets.

Does anyone have more experience in defining function in R and has any idea how to solve this? See my naive and failed attempts below.

Thanks a lot and best wishes, Jerg


Try1 using fsApply:

scale_fun <- scale(x, center = TRUE, scale = TRUE)
fs_scaled <- fsApply(fs_initial, FUN = scale, center = T, scale = TRUE, 
                     simplify = T,
                     use.exprs = T) 
 


Try2 using normalization:

scale_fun <- normalization(parameters = scale_para,  

                           normalizationId = "zScore", 

                           normFunction = scale, 
                           arguments = list("x=data", "center=T", "scale=T"))

fs_norm  <- normalize(data = fs_initial, x = scale_fun)

flowcore fcs normalization flowstats • 1.6k views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
(Private Address)

Then you simply pass your chosen columns as argument to 'FUN'

fs_scaled <- fsApply(fs_initial, FUN = function(fr, channels){
                                      mat <- exprs(fr)[, channels, drop = FALSE]

                                      exprs(fr)[, channels] <- scale(mat)

                                      fr
                                      }, channels = c("FSC-H", "SSC-H")
                                                                    ) 
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
(Private Address)

Try this

fs_scaled <- fsApply(fs_initial, FUN = function(fr){
                                      mat <- exprs(fr)
                                      exprs(fr) <- scale(mat)
                                      fr
                                      }) 

 

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Entering edit mode
BenAbflack • 0
@benabflack-8435
Last seen 6.2 years ago
Zurich/Switzerland

Thanks a lot Mike,

Your scheme worked, just had to find a workaround solution to only apply it to some chosen columns but in the end I just keep all of them.

Best, Jerg

 

 

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