mmgmos {mmgmos} | R Documentation |
This function converts an object of class AffyBatch
into an object of class
exprReslt
using the Multi-chip 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.
mmgmos(object, savepar=FALSE, eps=1.0e-6)
object |
an object of AffyBatch |
savepar |
Logical value. If TRUE the estimated parameters of the model are saved in file par.txt and phi.txt. |
eps |
Optimisation termination criteria. |
The obtained expression measures are in log base 2 scale.
An object of class exprReslt
.
Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence
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
Related class exprReslt-class
and related method mgmos
## 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<-mmgmos(affybatch.example)