bkgdCorrect {codelink} | R Documentation |
Takes a CodelinkSet or Codelink object with Spot mean and Bkgd median values and performes background correction using one of the methods available.
bkgdCorrect(object, method = "half", preserve = FALSE, verbose = FALSE, offset = 0) ## S4 method for signature 'CodelinkSet' codCorrect(object, method = "half", normexp.method="saddle", offset=0)
object |
an object of class CodelinkSet or Codelink. |
method |
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. |
normexp.method |
method used with normexp correction. |
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
data(codset) codset <- codCorrect(codset, method = "half")