bkgdCorrect {codelink} | R Documentation |
Takes a Codelink object with Spot mean and Bkgd median values and corrects applying one of the methods available.
bkgdCorrect(object, method = "half", preserve = FALSE, verbose = FALSE, offset = 0)
object |
character; an object of class "Codelink". |
method |
character; the correction method to use, one of "none", "subtract", "half" and "normexp". |
preserve |
logical; if Smean and Bmedian slots should be preserved. |
verbose |
logical; if TRUE print some information with method normexp. |
offset |
numeric; value to add to intensities. |
Available methods are: . none: left intensities untouched. . subtract: simple subtraction of Bkgd median from Spot mean. . half: the same as above but aboid negative values setting all intensity values below zero to 0.5. . normexp: apply normexp background adjustment from package limma.
An object of class Codelink with corrected intensity values, that is Ri slot.
Diego Diez
## Not run: data(codelink.example) codelink.example <- bkgdCorrect(codelink.example, method = "half") ## End(Not run)