R: Expression

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