normalize.AffyBatch.vsn {vsn} | R Documentation |
Wrapper for vsn
to be used as a normalization method in the package affy
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 medianpolish
), the logarithm to
base 2 needs to be taken.
An object of class AffyBatch
.
Wolfgang Huber mailto:w.huber@dkfz.de
### The example has been commented out because it takes a long time. ### Please also refer to the vignette. ## library(affy) ## library(affydata) ## data(Dilution) ### let affy know about vsn ## normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") ## es1 = expresso(Dilution[1:2], ## bg.correct = FALSE, ## bg correction is done by vsn ## normalize.method = "vsn", ## pmcorrect.method = "pmonly", ## summary.method = "medianpolish") ## es2 = expresso(Dilution[1:2], ## bgcorrect.method = "rma", ## normalize.method = "quantiles", ## pmcorrect.method = "pmonly", ## summary.method = "medianpolish") ## par(mfrow=c(2,2), pch=".") ### extract expression values ## x1 = exprs(es1) ## x2 = exprs(es2) ### scatter plot ## plot(x1, main="vsn: chip 3 vs 4") ## plot(x2, main="rma: chip 3 vs 4") ### rank(mean) - difference plot ## ylim = c(-0.7, 0.7) ## plot(rank(rowSums(x1)), diff(t(x1)), ylim=ylim, main="rank(mean) vs differences") ## abline(h=0, col="red") ## plot(rank(rowSums(x2)), diff(t(x2)), ylim=ylim, main="rank(mean) vs differences") ## abline(h=0, col="red")