R: Preprocess AffyBatch object for RPA.

RPA.preprocess {RPA}

R Documentation

Preprocess AffyBatch object for RPA.

Description

Quantile normalizes and log2-transforms the probe-level raw data in abatch. Then probe-level differential expression is computed between the specified 'control' array (cind) and the other arrays.

Usage

RPA.preprocess(abatch, cind)

Arguments

`abatch`	An AffyBatch object.
`cind`	Specifies which of the arrays in abatch is used as a control in computing probe-level differential expression.

Details

The probe-specific variance estimates are robust against the choice of cind; cind can be selected at random.

Value

`fcmat`	Probes x arrays preprocessed differential expression matrix.
`cind`	Specifies which array in abatch was selected as a control for computing probe-level differential expression.

Author(s)

Leo Lahti <leo.lahti@tkk.fi>

References

Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays. Lahti et al., TCBB/IEEE, to appear. See http://www.cis.hut.fi/projects/mi/software/RPA/