mgmos {mmgmos}R Documentation

modified gamma Model for Oligonucleotide Signal

Description

This function converts an object of class AffyBatch into an object of class exprReslt using the modified gamma Model for Oligonucleotide Signal (multi-mgMOS). This function obtains confidence of measures, standard deviation and 5, 25, 50, 75 and 95 percentiles, as well as the estimated expression levels.

Usage

mgmos(object, eps=1.0e-6)

Arguments

object an object of AffyBatch
eps Optimisation termination criteria.

Details

The obtained expression measures are in log base 2 scale.

Value

An object of class exprReslt.

Author(s)

Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence

References

Liu,X., Milo,M., Lawrence,N.D. and Rattray,M. (2005) A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips, technical report available upon request.

Milo,M., Niranjan,M., Holley,M.C., Rattray,M. and Lawrence,N.D. (2004) A probabilistic approach for summarising oligonucleotide gene expression data, technical report available upon request.

Milo,M., Fazeli,A., Niranjan,M. and Lawrence,N.D. (2003) A probabilistic model for the extractioin of expression levels from oligonucleotide arrays, Biochemical Society Transactions, 31: 1510-1512.

Peter Spellucci. DONLP2 code and accompanying documentation. Electronically available via http://plato.la.asu.edu/donlp2.html

See Also

Related class exprReslt-class and related method mmgmos

Examples

## load example data from package Affy
data(affybatch.example)

## use method mmgmos to calculate the expressiong levels and related confidence 
## of the measures for the example data
eset<-mgmos(affybatch.example)

[Package mmgmos version 1.2.0 Index]