R: Multi-chip modified gamma Model for Oligonucleotide Signal...
PMmmgmos
R Documentation
Multi-chip modified gamma Model for Oligonucleotide Signal using only PM probe intensities
Description
This function converts an object of class FeatureSet into an object of class
exprReslt using the Multi-chip modified gamma Model for Oligonucleotide Signal
(PMmulti-mgMOS). This method uses only PM probe intensites. This function obtains confidence of measures, standard deviation and 5,
25, 50, 75 and 95 percentiles, as well as the estimated expression levels.
Logical value. If TRUE, perform background correction before applying PMmmgmos.
replaceZeroIntensities
Logical value. If TRUE, replace 0 intensities with 1 before applying PMmmgmos.
gsnorm
character. specifying the algorithm of global scaling normalisation.
savepar
Logical value. If TRUE the estimated parameters of the model are saved in file par_pmmmgmos.txt
eps
Optimisation termination criteria.
addConstant
numeric. This is an experimental feature and should not generally be changed from the default value.
Details
The obtained expression measures are in log base 2 scale.
The algorithms of global scaling normalisation can be one of "median", "none", "mean", "meanlog".
"mean" and "meanlog" are mean-centered normalisation on raw scale and log scale respectively, and "median"
is median-centered normalisation. "none" will result in no global scaling normalisation being applied.
There are n+2 columns in file par_pmmmgmos.txt, n is the number of chips. The first n columns are 'alpha' values for n chips,
column n+1 is 'c' values and the final column is values for 'd'.
Value
An object of class exprReslt.
Author(s)
Xuejun Liu, Zhenzhu Gao, 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, Bioinformatics 21: 3637-3644.
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 mgmos
Examples
## Code commented out to speed up checks
## load example data from package pumadata
#if (require(pumadata)&&require(puma)){
# data(oligo.estrogen)
## use method PMmmgMOS to calculate the expression levels and related confidence
##of the measures for the example data
# eset<-PMmmgmos(oligo.estrogen,gsnorm="none")
#}