Description Usage Arguments Details Value Author(s) See Also Examples

Fit a model which describes the variation of the labeled internal standards from the biological factors.

1 | ```
standardsFit(object, factors, ncomp = NULL, lg = TRUE, fitfunc = lm, ...)
``` |

`object` |
an |

`factors` |
the biological factors described in the pheno data
slot if |

`ncomp` |
number of PCA components to use. Determined by
cross-validation if left |

`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 |

`...` |
passed on to |

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. Scaling is done outside the PCA 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

1 2 3 4 5 6 7 8 | ```
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)
``` |

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