normalize.AffyBatch.vsn {vsn} | R Documentation |
Wrapper for vsn
to be used as a normalization
method with the expresso function of the package affy. This is
deprecated, plus use justvsn
instead.
normalize.AffyBatch.vsn(abatch, subsample=20000, niter = 4, strata, ...)
abatch |
An object of type AffyBatch . |
subsample |
The number of probes to be sampled for the fit of the transformation parameters. |
niter |
Parameter passed on to vsn . |
strata |
Integer vector of length nrow(y). See
vsn for details. |
... |
Further parameters for vsn . |
Please refer to the "details" and "references" sections of the man page for
vsn
for more details about this method.
Important note: after calling vsn
, the function
normalize.AffyBatch.vsn
exponentiates the data. This is done in
order to make the behavior of this function similar to the other
normalization methods in affy. There, it is assumed that in subsequent
analysis steps (e.g. in medpolish
), the logarithm to
base 2 needs to be taken.
An object of class AffyBatch
.
Wolfgang Huber http://www.ebi.ac.uk/huber
## Please see vignette.