[BioC] Re: Normalization with cDNA array

[Simon Lin]

Joyce:



The choice of normalization is heavily depended on the biological
assumptions. Usually, I will do location normalization first, followed by
scale normalization. To clarify the assumptions behind, let us consider the
following extreme examples:

1) Suppose there is a drug affecting the OVERALL transcription activities.
As a consequence, ALL genes are expressed half as the level of normal
control. If we do location normalization, we will not see the effect of this
drug!

2) Suppose there is a drug that can modulate the expression of x number of
the genes on the chip. As a consequence, the magnitude of these x genes is
twice as normal control (no directional changes, just an amplitude change).
If we do a scale normalization, this effect might be erased and unseen.

3) Suppose we are using a focused array with only 100 apoptosis-related
genes. If drug X induces apoptosis, and thus most of the genes on this chip
are upregulated; we can find ourselves in a more difficult position.
Solutions include special controls for normalization.



Simon



=================================================
  Simon M. Lin, M.D.
  Manager, Duke Bioinformatics Shared Resource
  Assistant Research Professor, Biostatistics and Bioinformatics
  Box 3958, Duke University Medical Center
  Durham, NC 27710
  Ph: (919) 681-9646 FAX: (919) 681-8028
  Lin00025 (at) mc.duke.edu
  http://dbsr.duke.edu
=================================================



> Message: 1
> Date: Fri, 30 Jan 2004 09:02:04 -0600
> From: Joyce Gu <jwgu at bcm.tmc.edu>
> Subject: [BioC] Normalization with cDNA array
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <401A72AC at webmail.bcm.tmc.edu>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Hello,
> There are two ways to normalize the data, one is location normalization,
the
> other is scale normalization in marrayClasses. I am wondering what kind of
> situation should we use location normalization,and when should we use
scale
> normalization?
> Does anyone has any suggession?
>
> Thanks
>