Parameter Optimization for Flow Cytometry Data Transformation

Description

Maximum likelihood estimation of parameters for common flow cytometry data transformations.

Details

Index:

flowTrans               Optimizing transformations for flow cytometry
                        data

Author(s)

Greg Finak <greg.finak@ircm.qc.ca>, Juan Manuel-Perez <jperez@ircm.qc.ca>, Raphael Gottardo <raphael.gottardo@ircm.qc.ca>

Maintainer: Greg Finak <greg.finak@ircm.qc.ca>

References

Finak G, Perez J M, Weng A, Gottardo R. Optimizing Transformations for Flow Cytometry. (Submitted)

Examples

#Load some data
data(GvHD)
#transform the first sample, forward and side scatter.
result<-flowTrans(GvHD[[1]],"mclMultivArcSinh",colnames(GvHD[[1]])[1:2],n2f=FALSE,parameters.only=FALSE);
plot(result$result);
summary(result);

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(flowTrans)
Loading required package: flowCore
Loading required package: flowViz
Loading required package: lattice
Loading required package: flowClust
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:flowCore':

    normalize, sort

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: graph
Loading required package: RBGL
Loading required package: ellipse
Loading required package: mnormt
Loading required package: corpcor
Loading required package: clue

Attaching package: 'flowClust'

The following object is masked from 'package:graphics':

    box

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowTrans/flowTrans-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: flowTrans-package
> ### Title: Parameter Optimization for Flow Cytometry Data Transformation
> ### Aliases: flowTrans-package
> ### Keywords: package models optimize
> 
> ### ** Examples
> 
> #Load some data
> data(GvHD)
> #transform the first sample, forward and side scatter.
> result<-flowTrans(GvHD[[1]],"mclMultivArcSinh",colnames(GvHD[[1]])[1:2],n2f=FALSE,parameters.only=FALSE);
> plot(result$result);
There were 22 warnings (use warnings() to see them)
> summary(result);
Transformation: 
[1] "mclMultivArcSinh"
Transformed Results: 
flowFrame object 's5a01'
with 3420 cells and 8 observables:
      name              desc        range minRange     maxRange
$P1N FSC-H        FSC-Height     7.624613 4.787555     7.624613
$P2N SSC-H        SSC-Height     7.624613 2.644115     7.624613
$P3N FL1-H         CD15 FITC 10000.000000 1.000000 10000.000000
$P4N FL2-H           CD45 PE  9221.665909 1.000000  9221.665909
$P5N FL3-H        CD14 PerCP  1131.783715 1.000000  1131.783715
$P6N FL2-A              <NA>  1023.000000 0.000000  1023.000000
$P7N FL4-H          CD33 APC  1162.769539 1.000000  1162.769539
$P8N  Time Time (51.20 sec.)   755.000000 1.000000   755.000000
153 keywords are stored in the 'description' slot

Transformation parameters:
        a         b         c 
0.9999977 0.9999939 0.0000000 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>