## load example data
data(example.lumi)
## Quality control estimation
lumi.Q <- lumiQ(example.lumi)
## summary
summary(lumi.Q)
## plot the density
plot(lumi.Q, what='density')
## plot the pairwise sample correlation
plot(lumi.Q, what='pair')
## plot the pairwise MAplot
plot(lumi.Q, what='MAplot')
## sample relations
plot(lumi.Q, what='sampleRelation', method='mds', color=c('100US', '95US:5P', '100US', '95US:5P'))
## detect outlier based on the distance to the mean profile
plot(lumi.Q, what='outlier')
## Density plot of coefficient of variance
plot(lumi.Q, what='cv')
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 '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/plot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot-methods
> ### Title: Plot of a ExpressionSet object
> ### Aliases: plot-methods plot.ExpressionSet plot,ExpressionSet-method
> ### plot,ExpressionSet,missing-method
> ### Keywords: methods hplot
>
> ### ** Examples
>
>
> ## load example data
> data(example.lumi)
>
> ## Quality control estimation
> lumi.Q <- lumiQ(example.lumi)
Perform Quality Control assessment of the LumiBatch object ...
>
> ## summary
> summary(lumi.Q)
Summary of data information:
Illumina Inc. BeadStudio version 1.4.0.1
Normalization = none
Array Content = 11188230_100CP_MAGE-ML.XML
Error Model = none
DateTime = 2/3/2005 3:21 PM
Local Settings = en-US
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 21:31:10 2016-07-06 21:31:10
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
Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 8000 features, 4 samples
element names: beadNum, detection, exprs, se.exprs
protocolData: none
phenoData
sampleNames: A01 A02 B01 B02
varLabels: sampleID label
varMetadata: labelDescription
featureData
featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ...
33KnLHy.RFaieogAF4 (8000 total)
fvarLabels: TargetID
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanAll.db
Control Data: Available
QC information: Please run summary(x, 'QC') for details!
>
> ## plot the density
> plot(lumi.Q, what='density')
>
> ## plot the pairwise sample correlation
> plot(lumi.Q, what='pair')
>
> ## plot the pairwise MAplot
> plot(lumi.Q, what='MAplot')
>
> ## sample relations
> plot(lumi.Q, what='sampleRelation', method='mds', color=c('100US', '95US:5P', '100US', '95US:5P'))
>
> ## detect outlier based on the distance to the mean profile
> plot(lumi.Q, what='outlier')
>
> ## Density plot of coefficient of variance
> plot(lumi.Q, what='cv')
>
>
>
>
>
>
> dev.off()
null device
1
>