| averageQuantile.AffymetrixCelSet {aroma.affymetrix} | R Documentation |
Calculates the average empirical distribution across all samples.
## S3 method for class 'AffymetrixCelSet': averageQuantile(this, probes=NULL, excludeCells=NULL, ..., verbose=FALSE)
probes |
An optional numeric vector specifying what subset of
probes to be used to calculate the empirical distribution.
If NULL, all probes are used. |
... |
Not used. |
verbose |
See Verbose. |
This methods implements Step A2-A3 in the algorithm for quantile normalization proposed by Bengtsson et al. (2008).
Returns a double vector of length N.
If NAs are detected in a sample, these are excluded and the
approx() function (approx) is used to "expand"
the vector of the remaining values so that the sorted vector
(still) have length N.
Henrik Bengtsson (http://www.braju.com/R/)
[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.
averageQuantile.list
For more information see AffymetrixCelSet.