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 !
Amelie
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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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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
> >
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
[[alternative HTML version deleted]]
Hi Amelie:
You can use gcRMA to normalize your raw data. Your duplicates can
be
"grouped" when you perform differential expression analysis using
packages such as Limma which will fit linear models for each gene.
Hope this helps.
Cheers,
Wei
ab19 at 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 !
>
> Amelie
>
>
>
>