On Dec 4, 2007 12:21 AM, Seungwoo Hwang <swhwang10@yahoo.com> wrote:

> I have a conceptual question on normalization of replicate arrays.
>
> Let's say I have several replicate arrays. I wonder whether it is
> advisable or not to apply different normalization methods to each of
> the replicate arrays. Let me illustrate with the following two
> situations.
>
> (1) By inspecting the raw data, some arrays look as if they need
> print-tip lowess while the other arrays look as if global lowess
> suffice. Then can I do print-tip lowess to some and global lowess to
> others? Or is it advisable to apply print-tip lowess to all replicate
> arrays consistently?
>
> (2) By inspecting the raw data, some arrays look as if they need
> print-tip scale normalization while the other arrays look as if no such
> scaling is needed. Then can I do scaling to some and no scaling to
> others? Or it is advisable to apply print-tip scaling to all replicate
> arrays consistently?
>
> >From the archive I found a previous post implying consistent
> normalization to replicate arrays.
> To quote it: "Normalization together presumes that the conditions were
> essentially the same and separate normalization allows them to be
> different. When they are the same, then separate normalization will
> almost surely be a bit less efficient (in a statistical sense) and when
> they are really different joint normalization can be very problematic."
>
> However, if I normalize the replicate arrays with the same method
> altogether, wouldn't it be not advisable either because doing so may
> remove true biological signals present in the "other" replicate arrays?
> For example, in (1), I think that print-tip lowess normalizing the
> arrays that seemingly need only global lowess may remove true
> biological signals that present in those arrays. Similar arguments may
> hold for (2).
>
> In summary, I would like to know which approach is more advisable: (A)
> normalizing all replicate arrays using the same method consistently
> regardless of differences observed among the replicate arrays, or (B)
> using whatever normalization method that best suits each of the
> replicate arrays.
>

Hi, Seungwoo.  I think you are best to stick with (A).  That said, it sounds
like you might want to consider looking closely at the quality of the arrays
to see if all the arrays should be included in further analysis since they
may be of significantly varying quality.  There are no "rules" that I know
of to judge "absolutely" the quality of an array, but there are numerous
tools in bioconductor for examining it.

Sean

	[[alternative HTML version deleted]]

