mmgmos {puma} | 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 , background=FALSE , replaceZeroIntensities=TRUE , gsnorm=c("median", "none", "mean", "meanlog") , savepar=FALSE , eps=1.0e-6 , orig.phis = FALSE , addConstant = 0 )
object |
an object of AffyBatch |
background |
Logical value. If TRUE , perform background correction before applying mmgmos. |
replaceZeroIntensities |
Logical value. If TRUE , replace 0 intensities with 1 before applying mmgmos. |
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_mmgmos.txt and phi_mmgmos.txt. |
eps |
Optimisation termination criteria. |
orig.phis |
Logical value. If TRUE , use phi values created from hgu95a array. |
addConstant |
numeric. This is an experimental feature and should not generally be changed from the default value. |
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 2*n+2 columns in file par_mmgmos.txt, n is the number of chips. The first n columns are 'alpha' values for n chips, the next n columns are 'a' values for n chips, column 2*n+1 is 'c' values and the final column is values for 'd'. The file phi_mmgmos.txt keeps the final optimal value of 'phi'.
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, 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
Related class exprReslt-class
and related method mgmos
## Code commented out to speed up checks ## load example data from package affydata # if (require(affydata)) data(Dilution) ## use method mmgMOS to calculate the expression levels and related confidence ## of the measures for the example data #eset<-mmgmos(Dilution)