Quality control evaluation of the LumiBatch object

Description

Quality control evaluation of the LumiBatch object and returns a summary of the data

Usage

lumiQ(x.lumi, logMode = TRUE, detectionTh = 0.01, verbose = TRUE)

Arguments

Details

Quality control of a LumiBatch object includes estimating the mean and standard deviation of the chips, detectable probe ratio of each chip, sample (chip) relations, detecting outliers of samples (chips). The produced QC information is kept in the QC slot of LumiBatch class. The summary function will provide a summary of the QC information (See example).

Value

a LumiBatch object with QC slot keeping the QC information

Author(s)

Pan Du

See Also

LumiBatch, plot,ExpressionSet-method

Examples

## load example data
data(example.lumi)

## Do quality control estimation
lumi.Q <- lumiQ(example.lumi)

## A summary of the QC
summary(lumi.Q, 'QC')

## Plot the results
## plot the pairwise sample correlation
plot(lumi.Q, what='pair')

## see more examples in "plot,ExpressionSet-method" help documents

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(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/lumiQ.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiQ
> ### Title: Quality control evaluation of the LumiBatch object
> ### Aliases: lumiQ
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> 
> ## Do quality control estimation
> lumi.Q <- lumiQ(example.lumi)
Perform Quality Control assessment of the LumiBatch object ...
> 
> ## A summary of the QC
> summary(lumi.Q, 'QC')
Data dimension:  8000 genes x 4 samples 

Summary of Samples:
                            A01    A02     B01     B02
mean                     8.3250  8.565  8.2570  8.3470
standard deviation       1.5640  1.693  1.7280  1.6760
detection rate(0.01)     0.5432  0.564  0.5774  0.5758
distance to sample mean 22.4200 26.920 24.6000 21.0900

Major Operation History:
            submitted            finished
1 2007-04-22 00:08:36 2007-04-22 00:10:36
2 2007-04-22 00:10:36 2007-04-22 00:10:38
3 2007-04-22 00:13:06 2007-04-22 00:13:10
4 2007-04-22 00:59:20 2007-04-22 00:59:36
5 2016-07-06 21:29:30 2016-07-06 21:29:30
                                             command lumiVersion
1           lumiR("../data/Barnes_gene_profile.txt")       1.1.6
2                             lumiQ(x.lumi = x.lumi)       1.1.6
3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1")       1.1.6
4            Subsetting 8000 features and 4 samples.       1.1.6
5                       lumiQ(x.lumi = example.lumi)      2.24.0
> 
> ## Plot the results
> ## plot the pairwise sample correlation
> plot(lumi.Q, what='pair')
> 
> ## see more examples in "plot,ExpressionSet-method" help documents
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>