On Fri, Mar 27, 2009 at 7:07 AM, <ab19@sanger.ac.uk> wrote:

> Dear Sean,
>
> Thank you for your answer. I understand that you need replicates when you
> work with differential expression in order to assess the the variance
> between them and compare it then with the "inter" variance. My purpose is
> not to perform a differential expression analysis. Still, is it good to
> loose the information that replicates may provide but using only one of
> them ?
>

Generally, you'll want to use all the samples that meet quality criteria.
And it is probably not useful to do things like "averaging" replicates and
the like.

If you need more details, then you might explain what you are trying to
accomplish.

Sean



>
> Thanks for your help !
>
> Amelie
>
> > On Fri, Mar 27, 2009 at 6:04 AM, <ab19@sanger.ac.uk> wrote:
> >
> >> Hello,
> >>
> >> I am working with a set of Affymetrix arrays, all of the same type,
> >> among
> >> which there is for each sample a biological duplicate. I was wondering
> >> when I should "group" the duplicates : before normalizing ? After ? I
> >> can't either find how to do it properly, do you have suggestions ?
> >>
> >> Thanks a lot for the help you may provide !
> >>
> >
> > Hi, Amelie.
> >
> > You'll want to deal with the replicates only when you are dealing with
> > differential expression.  See, for example, the limma user guide which
> has
> > some examples of interest.
> >
> > Sean
> >
>
>
>
>
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