Computing the Z' factor

Description

Computes the Z' factor per plate for a complete dataset file and plots the results.

Usage

ZPRIMEQualControl(header, data, channel, plotTitle, showPlot)

Arguments

Value

Returns the Z' values in the shell for each plate and saves them in a text file. The name of the text file will be the concatenation of the experiment name specified in the header and the character string "Z'Scores.txt".

Shows a plot of the Z' factor values and saves it as a png and a pdf file under the experiment name specified in the header concatenated with the function argument plotTitle.

The function returns a list containing:

References

J. Zhang, T. Chung, and K. Oldenburg. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen, 4:67-73, 1999.

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

res <- ZPRIMEQualControl(header, dataset, "SigIntensity", "Z' factors per plate", 1)
zprime_plot <- res[[1]]
zprime_table <- res[[2]]

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.
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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(RNAither)
Loading required package: topGO
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

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    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

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: GO.db
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Attaching package: 'S4Vectors'

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    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

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    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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Loading required package: RankProd
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Attaching package: 'grid'

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Loading required package: rrcov
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Attaching package: 'robustbase'

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


Attaching package: 'RNAither'

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    trim

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAither/ZPRIMEQualControl.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ZPRIMEQualControl
> ### Title: Computing the Z' factor
> ### Aliases: ZPRIMEQualControl
> ### Keywords: arith
> 
> ### ** Examples
> 
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
> 
> res <- ZPRIMEQualControl(header, dataset, "SigIntensity", "Z' factors per plate", 1)
[1] 
[1] The Z'Score for Experiment 1 Plate 1 is -0.573704732277928
[1] The Z'Score for Experiment 1 Plate 2 is -0.526288362369338
[1] The Z'Score for Experiment 2 Plate 1 is -1.50964793133475
[1] The Z'Score for Experiment 2 Plate 2 is 0.0730893516094138
[1] 
> zprime_plot <- res[[1]]
> zprime_table <- res[[2]]
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>