[BioC] help in normalization cDNA arrays
J.delasHeras at ed.ac.uk
J.delasHeras at ed.ac.uk
Wed Jan 24 17:16:46 CET 2007
If you're going to be looking at the ratios only, normalising between
arrays is rarely going to change anything (as the method aims to scale
the range of intensities while leaving the ratios relatively unchanged).
You can easily do a quick test and compare the results you get if you
don't normalise between arrays, and using different methods (scale and
Aquantile, for instance). When I try, I don't see much difference at
all. I try to avoid altering the data (normalising procedures alter
the data) unless I have a good reason to do so.
On teh other hand, if you want to do some sort of single channel
analysis, where you compare signal from one slide to signal from
another, then you do need to make sure the slides are all in the same
scale, and normalising between arrays makes sense.
Also, as someone else said, you should not normalise between arrays
experiments that by their own nature will behave very differently.
I think that when we start doing arrays we tend to think
"we-must-normalise... we-must-normalise" (imagine that with a Dalek
voice ;-) and that anything that uses teh word "normalisation" is a
good thing. However, it all depends on the biology of our experiment.
Try to understand what your experiments are about and what is
expected, and then think how it would make sense to normalise the
data. Then see which of the methods available to you do what is
necessary for your data. I find it useful to explore teh raw data
(scatter plots, MA plots) and see what the trends are... and when I
decide to normaise in a particular way, copmpare the effect of the
normalisation to see if it did what I (roughly) wanted it to do. This
allows you to build up a good feel for what the limitations are with
any method, and you truly get to know your data.
Jose
Quoting Marcelo Laia <marcelolaia at gmail.com>:
> Hi,
>
> I did a
>
> normalizeWithinArrays(RG,method="printtiploess")
>
> and get this boxplot
>
> http://200.145.102.65:9102/normalized.data.png
>
> Is needed to do a
>
> normalizeBetweenArrays(MA.2,method="scale")
>
> ???
>
> What you suggest me?
>
> I am not sure if a little difference between box is big or not.
>
> Thank you
>
> --
> Marcelo Luiz de Laia
> Ph.D Candidate
> São Paulo State University (http://www.unesp.br/eng/)
> School of Agricultural and Veterinary Sciences
> Department of Technology
> Via de Acesso Prof. Paulo Donato Castellane s/n
> 14884-900 Jaboticabal - SP - Brazil
> Phone: +55-016-3209-2675
> Cell: +55-016-97098526
>
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--
Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
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