[R-sig-ME] varFixed function query in lme

[Ben Bolker]

Douglas Bates <bates at ...> writes:

> 
> It is best to send inquiries like this to the
> R-SIG-Mixed-Models at ... mailing list ...

  [snip]

> On Mon, Oct 13, 2014 at 8:46 AM, David Cox <dac64 at ...> wrote:
> 
> > Dear Professor Bates,
>

[snip]

> > I'm using lme to model the peptide sequences of a set of proteins for
> > cancer patients and healthy individuals. I want to
>  use the weights function
> > so that the peptide intensities are inversely weighted
> with the variance.
> > The higher the variance, the lower the weighting etc. As the peptide
> > intensities of cancer patients and healthy individuals
>  will be different, I
> > want to apply this weighting separately for each group.
> >
> > At the moment I've tried with a model like this for the 1st protein:
> >  Peptide Intensities ~ Covariates + Peptide Sequences + Group, random =
> > Sample Id, data = data, weights = ~ Group

  Shouldn't this be something like

  weights= varIdent(~1|Group)

?

I don't see that a raw formula will work in the "weights" function.
Picking up a copy of Pinheiro and Bates 2000 might be a good idea ...

  Ben Bolker