standardsFit {crmn} | R Documentation |
Fit a model which describes the variation of the labeled internal standards from the biological factors.
standardsFit(object, factors, ncomp, lg=TRUE, fitfunc=lm, ...)
object |
an ExpressionSet or a matrix .
Note that if you pass amatrix have to specify the identity of
the standards by
passing the appropriate argument to standards . |
factors |
the biological factors described in the pheno data slot |
ncomp |
number of PCA components to use.
Determined by cross-validation if left NULL |
lg |
logical indicating that the data should be log transformed |
fitfunc |
the function that creates the model fit for normalization, must use the same interfaces as lm . |
... |
passed on to Q2 , pca , standards and analytes |
There is often unwanted variation in among the labeled internal standards which is related to the experimental factors due to overlapping peaks etc. This function fits a model that describes that overlapping variation using a scaled and centered PCA / multiple linear regression model.
a list containing the PCA/MLR model, the recommended number of components for that model, the standard deviations and mean values and Q2/R2 for the fit.
Henning Redestig henning@psc.riken.jp
makeX
, standardsPred
data(mix) sfit <- standardsFit(mix, "type", ncomp=3) slplot(sfit$fit$pc) ## same thing Y <- exprs(mix) G <- model.matrix(~-1+mix$type) isIS <- fData(mix)$tag == 'IS' sfit <- standardsFit(Y, G, standards=isIS, ncomp=3)