lumiQ {lumi} | R Documentation |
lumiQ(x.lumi, logMode = TRUE, detectionTh = 0.01)
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 |
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).
a LumiBatch object with QC slot keeping the QC information
Pan Du
LumiBatch
, plot,LumiBatch-method
## 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,LumiBatch-method" help documents