normalize {codelink} | R Documentation |
Takes a CodelinkSet or Codelink object and applies normalization to intensity values.
## S4 method for signature 'Codelink' normalize(object, method="quantiles", log.it=TRUE, preserve=FALSE, weights=NULL, loess.method="fast") ## S4 method for signature 'CodelinkSet' normalize(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast") ## S4 method for signature 'CodelinkSet' codNormalize(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast")
object |
an object of class CodelinkSet or Codelink. |
method |
method to use in normalization. |
log.it |
logical; if data should be log2. |
preserve |
logical; if Ri slot should be preserved. |
weights |
weights for method CyclicLoess. |
loess.method |
loess method to be used, default to 'fast'. |
Currently supported methods include "median", "quantile" and "loess". Normalization functions are borrowed from the limma package.
If a matrix of weights is passed for CyclicLoess normalization, a vector is constructed taking the lowest weight for each probe.
A CodelinkSet or Codelink object with normalized intensity values.
Diego Diez
data(codset) # Background correction. codset <- codCorrect(codset, method = "half") # Normalization. codset <- normalize(codset, method = "quantile")