[BioC] normalization across sites

[Weiwei Shi]

Then does it mean between-lab variation and between-sample (in one
lab) variation could be treated w/o knowing that? I feel there might
be more than that.

On 6/21/07, Kasper Daniel Hansen <khansen at stat.berkeley.edu> wrote:
> Yes, you could do that.
>
> What Sean is alluding to, is the fact that there is usually a large
> between-lab variation. Some times this variation is greater than the
> biological variation. If you are downloading from a website (or for
> that matter anyway) you should do proper QC of the chips, because you
> will have little idea of what the original people did with it and
> whether they made good choices.
>
> In principle, if the hybes are good and you use proper normalization,
> hopefully you will get results that are comparable from lab to lab.
> But this is not at all given, and you need to be careful when you do
> these things.
>
> Kasper
>
>
> On Jun 21, 2007, at 6:51 PM, Weiwei Shi wrote:
>
> > Ok, if I understand correctly, I should combine two sources of data
> > and run RMA on it?
> >
> > On 6/21/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> >> Weiwei Shi wrote:
> >>> Hi,
> >>>
> >>> Suppose that I have two sets of arrays, both of which use the same
> >>> platform. My question is, if I have datasets which have been
> >>> preprocessed, what's the best way for me to normalize them.
> >>> Currently
> >>> I just scale them sample-wise; but not sure of it.
> >>>
> >>> Otherwise, should I go back to .CEL file? But how to proceed from
> >>> there?
> >>>
> >> Start from raw data, yes.  You may need to use an ANOVA or linear
> >> model
> >> to deal with confounding variables.  Quality control is especially
> >> important.
> >>
> >> Sean
> >>
> >
> >
> > --
> > Weiwei Shi, Ph.D
> > Research Scientist
> > GeneGO, Inc.
> >
> > "Did you always know?"
> > "No, I did not. But I believed..."
> > ---Matrix III
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/
> > gmane.science.biology.informatics.conductor
>
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III