Dear Wolfgang and Gordon,

thanks a lot for the help!

Artur

On 9/16/07, Wolfgang Huber <huber@ebi.ac.uk> wrote:
>
> Dear Gordon,
>
> great - thanks for pointing this out! Just to explain the rationale for
> "vsn" objects:
>
> "vsn" objects are returned by the function "vsn2" and contain all the
> information on the fit of the vsn model to data. There is a "predict"
> method that lets users apply the fitted model to either the same or new
> data (e.g. if you use known housekeeping or spike-in transcrips for
> fitting and then apply to all data).
>
> In many use cases, one just wants to use the normalized & transformed
> data and not bother with the details of vsn.  The wrapper "justvsn" is
> for that purpose, it returns an ExpressionSet or NChannelSet, as
> appropriate.
>
> In vsn version 1, I had tried to mush the fit results and diagnostics
> into the returned exprSet object, but that never really worked well,
> hence it is now done as described above.
>
>   Best wishes
>         Wolfgang
>
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
> >
> >
> > Hi Wolfgang,
> >
> > Actually there is an as.matrix method for vsn objects in the limma
> > package, it just had a bug. Now fixed.
> >
> > Best wishes
> > Gordon
> >
> >> [BioC] Problem with "as.matrix.vsn" and "duplicateCorrelation"
> fromlimma
> >>
> >>
> >>
> >> Wolfgang Huber
> >> <mailto:
> bioconductor%40stat.math.ethz.ch?Subject=%5BBioC%5D%20Problem%20with%20%22as.matrix.vsn%22%20and%20%22duplicateCorrelation%22%0A%20from%09limma&In-Reply-To=3aa934e00709151315m371c208dleea83bf372da2aaa%40mail.gmail.com
> >huber
> >> at ebi.ac.uk
> >> Sun Sep 16 02:07:38 CEST 2007
> >>
> >> Dear Artur,
> >>
> >> there is no "as.matrix" function for objects of type "vsn", such as
> >> returned by the "vsn2" function. You are right to use the "exprs"
> >> accessor instead.
> >>
> >> If you are looking for a wrapper to vsn2 that produces an ExpressionSet
> >> (rather than a vsn object), please look at "justvsn" (in the devel
> >> branch, will be in the bioc 2.1 release).
> >>
> >> Best wishes
> >>         Wolfgang
> >>
> >> > Hi all,
> >> >
> >> > I just wanted to report an error that I've been geting:
> >> > When I run duplicateCorrelation on this vsn object I get an error
> >> message.
> >> > If instead of using the vsn object I use the result of an "expres(
> >> > vsn.object)" function call it apparently works.
> >> > I could be mistaken, but I don't think that I upgraded my packages
> >> or R and
> >> > duplicateCorrelation after the last time I used duplicateCorrelation
> >> > succesfully.
> >> >
> >> > Thanks a lot!
> >> >
> >> > Artur Veloso
> >> >
> >> > Masters in Marine Biology Candidate
> >> > College of Charleston, South Carolina, USA
>
>
>

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