averageQuantile.AffymetrixCelSet | 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 |
... |
Not used. |
verbose |
See |
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 NA
s 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
[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
.
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