Estimate the coefficient of variance matrix of LumiBatch object

Description

Estimate the coefficient of variance matrix of LumiBatch object for each measurement or probe.

Usage

estimateLumiCV(x.lumi, type = c("measurement", "probe"), ifPlot = FALSE, ...)

Arguments

Details

By default, the coefficient of variance is the ratio of the mean and variance of the bead expression values. Basically, it is the ration of exprs and se.exprs element of LumiBatch object. If the type is "probe", it is the ratio of the mean and variance of probe expression profile.

Value

A matrix of coefficient of variance

Author(s)

Pan Du

See Also

lumiQ

Examples

## load example data
data(example.lumi)

## estimate the coefficient of variance and plot the density plot of it
cv <- estimateLumiCV(example.lumi, ifPlot = TRUE)

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(lumi)
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/estimateLumiCV.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateLumiCV
> ### Title: Estimate the coefficient of variance matrix of LumiBatch object
> ### Aliases: estimateLumiCV
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> 
> ## estimate the coefficient of variance and plot the density plot of it
> cv <- estimateLumiCV(example.lumi, ifPlot = TRUE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>