FACS data for cell-based apoptosis assay

Description

Set of FCS 3.0 files containing FACS data for each well of a 96 well microtitre plate

Format

map and apoptosis are directories, each containing 96 FCS 3.0 files derived from a FACS experiment to characterize effectors of the MAP-Kinase and apoptotic pathways, respectively. The files may be imported using function readFCS (for single files) or function readCytoSet (for all files in the directory).

Source

Mamatha Sauermann (apoptosis), Meher Majety (MAP-Kinase), both at DKFZ Heidelberg

See Also

readFCS, readCytoSet

Examples

apo <- readFCS(system.file("extdata", "apoptosis",
           "test2933T3.A01", package="facsDorit"))
apo
exprs(apo[1:3,])
description(apo)[3:6]

map <- readFCS(system.file("extdata", "map",
           "060304MAPK_controls.A01", package="facsDorit"))
map
exprs(map[1:3,])
description(map)[3:6]

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(facsDorit)
Loading required package: prada
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: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: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

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

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/facsDorit/facsDorit.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Apoptosis and MAP-Kinase example data
> ### Title: FACS data for cell-based apoptosis assay
> ### Aliases: facsDorit
> 
> ### ** Examples
> 
> apo <- readFCS(system.file("extdata", "apoptosis",
+            "test2933T3.A01", package="facsDorit"))
> apo
cytoFrame object with 20000 cells and 8 observables:
FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
slot 'description' has 148 elements
> exprs(apo[1:3,])
     FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
[1,]   275   299    85   612   169    50   381    0
[2,]   560   275   122   555   143    31   592    0
[3,]    87   156   196   544   117    35   656    0
> description(apo)[3:6]
                        $NEXTDATA                              $SYS 
                              "0" "Macintosh System Software 9.2.2" 
                          CREATOR                              $TOT 
        "CellQuest Pro<aa> 4.0.2"                           "20000" 
> 
> map <- readFCS(system.file("extdata", "map",
+            "060304MAPK_controls.A01", package="facsDorit"))
> map
cytoFrame object with 210 cells and 8 observables:
FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
slot 'description' has 146 elements
> exprs(map[1:3,])
     FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
[1,]   651   409    67   711   234   139   620   36
[2,]   235  1023   140   424    96     0   582   36
[3,]   543   378   244   755   220   193   580   36
> description(map)[3:6]
                        $NEXTDATA                              $SYS 
                              "0" "Macintosh System Software 9.2.2" 
                          CREATOR                              $TOT 
        "CellQuest Pro<aa> 4.0.2"                             "210" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>