[BioC] correlation between M values of replicate arrays

[Claus Mayer]

Dear João!

Most normalisation methods assume that the majority of genes are not 
differentially expressed, i.e. that there expected M value is 0. If this 
assumption is correct properly normalized data will show only weak 
correlation between M values from different arrays, so observing this in 
your normalised data is not necessarily a reason to worry.

There are different reasons why the unnormalized arrays might show 
higher correlations. The most obvious situation that comes to my mind is 
if you use something like a reference design, i.e you always have a 
control on dye1 and the treamtment sample on dye2. The intensity 
depending dye bias (which you try to remove with loess normalisation) 
will then automatically lead to correlated M values.
It is an unwanted correlation though, caused by a systematic bias, so 
the normalized data with less correlation are "better" in this case. 
There will be other scenarios where something like that happens, but 
without knowing details about your experiment it makes little sense to 
speculate about them.

Hope that helps

Claus

João Fadista wrote:
> Dear all,
> 
> I have some questions that I would like to pose to this list.
> 
> When I normalize microarray data (usually with the methods in
> normalizeWithinArrays function in limma package) I decrease the
> correlation between the M values of my replicate arrays. This
> obviously has an explanation bacause if we normalize "within" arrays,
> the differences between them tend to become larger. Therefore, if the
> correlation between replicates decrease, it seems like if we
> normalize our data we would get "worse" data.
> 
> Is this true? Does it happen the same to you? And how do you deal
> with that?
> 
> 
> 
> Med venlig hilsen / Regards
> 
> João Fadista Ph.d. studerende / Ph.d. student
> 
> 
>  AARHUS UNIVERSITET / UNIVERSITY OF AARHUS Det
> Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences 
> Forskningscenter Foulum / Research Centre Foulum Genetik og
> Bioteknologi / Dept. of Genetics and Biotechnology Blichers Allé 20,
> P.O. BOX 50 DK-8830 Tjele  Tel:	 +45 8999 1900 Direct:	 +45 8999 1900
>  Mobile:	 +45 E-mail:	 Joao.Fadista at agrsci.dk
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-- 
***********************************************************************************
  Dr Claus-D. Mayer                    | http://www.bioss.ac.uk
  Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
  Rowett Research Institute            | Telephone: +44 (0) 1224 716652
  Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349