vsn2
to be used as a normalization
method with the expresso function of the package affy. The expresso
function is deprecated, consider using justvsn
instead. The normalize.AffyBatch.vsn can still be useful on its own,
as it provides some additional control of the normalization process
(fitting on subsets, alternate transform parameters). normalize.AffyBatch.vsn( abatch, reference, strata = NULL, subsample = if (nrow(exprs(abatch))>30000L) 30000L else 0L, subset, log2scale = TRUE, log2asymp=FALSE, ...)
AffyBatch
.vsn2
for details.vsn2
.vsn2
.AffyBatch
.
The vsn
object returned, which can be used as reference
for
subsequent fits, is provided by
description(abatch)@preprocessing$vsnReference
.
vsn2
for more details about this method. Important note: after calling vsn2
, the function
normalize.AffyBatch.vsn
exponentiates the data (base 2).
This is done in order to make the behavior of this function similar to the
other normalization methods in affy. That packages uses the convention
of taking the logarithm to base in
subsequent analysis steps (e.g. in medpolish
).
vsn2