Expression

Description

Computes expression measures for probe level data

Usage

express(x, method=c("avglogpm", "li.wong", "avdiff"), normalize=T,
        normalize.method=c("quantile", "loess", "contrasts"), span=2/3,
        choose.subset=T, subset.size=5000, verbose=T, maxit=1)

Arguments

x a probe.level.object
method which method to use to compute measure of expression, "avglogpm", "li.wong", or "avdiff".
normalize logical value. If TRUE normalize probe level data before computing expression measures.
normalize.method which normalization method to use, "quantile", "loess" or "contrasts".
span loess span to use with "loess" and "contrast" methods
choose.subset logical value. For the "loess" and "contrast" methods, if TRUE it will do normalization on a subset and predict.
subset.size size of subset to use in normalization.
verbose logical value. If TRUE it writes out some messages.
maxit maximum number of iterations to use in method "loess".

Details

"avglogpm" is the recommended method. It uses a background corrected average of PM values as a measure of expression. "li.wong" uses the Li and Wong algorithm. "avdiff" uses Genechip's average difference.

Value

A matrix with expression values (genes represented by rows)

Author(s)

Rafael A. Irizarry

References

Irizarry, RA, Hobbs, B, and Speed, T (2001) http://biosun01.biostat.jhsph.edu/~ririzarr/papers/index.html

See Also

li.wong, avdiff