normalize {codelink} | R Documentation |
Takes a Codelink object and applies normalization to intensity values.
normalize(object, method = "quantiles", log.it = TRUE, preserve = FALSE, weights = NULL, verbose = FALSE)
object |
an object of class "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 vector for method CyclicLoess. |
verbose |
should informative output be printed. |
Currently supported methods include "loess", "quantiles" and "median". Median normalization is analogous to the default method applied for the manufacturer in the Codelink software. Loess is a modified version of CyclicLoess implemented in the affy package, allowing missing values and weights. Quantile normalization uses the normalizeQuantiles() function in the limma package.
A Codelink object with normalized intensity values.
Diego Diez
## Not run: data(codelink.example) # Background correction. codelink.example <- bkgdCorrect(codelink.example, method = "half") # Normalization. codelink.example <- normalize(codelink.example, method = "quantile") ## End(Not run)