aroma.affymetrix (version 3.0.0)

averageQuantile.AffymetrixCelSet: Calculates the average empirical distribution across all samples

Description

Calculates the average empirical distribution across all samples.

Usage

"averageQuantile"(this, probes=NULL, excludeCells=NULL, ..., verbose=FALSE)

Arguments

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.

Value

Returns a double vector of length N.

Missing values

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.

Details

This methods implements Step A2-A3 in the algorithm for quantile normalization proposed by Bengtsson et al. (2008).

References

[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.

See Also

averageQuantile.list For more information see AffymetrixCelSet.