lumiExpresso {lumi} | R Documentation |
Goes from raw Illumina probe intensities to expression values
lumiExpresso(lumiBatch, bg.correct = TRUE, bgcorrect.param = list(method='bgAdjust'), variance.stabilize = TRUE, varianceStabilize.param = list(), normalize = TRUE, normalize.param = list(), QC.evaluation = TRUE, QC.param = list(), verbose = TRUE)
lumiBatch |
a LumiBatch object, which can be the return of lumiR |
bg.correct |
a boolean to decide whether to do background correction or not |
bgcorrect.param |
a list of parameters of lumiB |
variance.stabilize |
a boolean to decide whether to do variance stabilization or not |
varianceStabilize.param |
a list of parameters of lumiT |
normalize |
a boolean to decide whether to do normalization or not |
normalize.param |
a list of parameters of lumiN |
QC.evaluation |
a boolean to decide whether to do quality control estimation before and after preprocessing |
QC.param |
a list of parameters of lumiQ |
verbose |
a boolean to decide whether to print out some messages |
The function is to encapsulate the major functions of Illumina preprocessing. It is organized in a similar way as the expresso
function in affy package.
return a processed LumiBatch object. The operation history can be track in the history slot of the object.
Pan Du
## load example data data(example.lumi) ## Do all the default preprocessing in one step lumi.N <- lumiExpresso(example.lumi) ## Do customized preprocessing. No variance stabilizing or log transform, use Quantile normalization. lumi.N <- lumiExpresso(example.lumi, variance.stabilize=FALSE, normalize.param = list(method='quantile'))