lumiQ: Quality control evaluation of the LumiBatch object

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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

x.lumi	a LumiBatch object
logMode	transform as log2 or not (the function can check whether it is already log transformed.)
detectionTh	the detection threshold used by detectionCall
verbose	a boolean to decide whether to print out some messages

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

lumi documentation built on Nov. 8, 2020, 5:27 p.m.