[BioC] Positive correlation between dye-swap technical replicates

[Philip Lijnzaad]

> In limma manual it is written that correlation should be negative for 
> dye swaps- why is it positive?- is it a question of wrong model matrix 
> or is it something wrong with my samples?

I concur with Juan Pedro that the most likely cause of this problem is 
mislabeling of the data; often they are already 'swapped back' for 
convenience, which is of course wrong. 

Regarding dye-bias, it would have be to really extreme to get the thing
you're seeing. 
 
But more generally, if you are worried  about gene-specific dyebias (and 
basically everyone should be), you could take a look at the dyebias package. 
It implements a method published recently by us (Margaritis et al., Mol. Sys. 
Biol. 2009, doi:10.1038/msb.2009.21). 

You can use the dyebias package to (1) recognize if there is any gene-specific 
dyebias; (2) which genes are affected most badly; (3) which slides are 
affected most badly; and (4) to correct it. Including a Dye effect in Limma 
is useful, but not enough: linear models cannot cope with the fact that the 
dye bias artefact depends not only on the gene, but also on the hybridization 
(for details, see the paper). The latter was not realized previously.

We frequently achieve variance reductions of M of over 50%. The only 
prerequisite is a set of dye-swaps. If you run into difficulties using the 
package, please feel free to drop me a line. 

Regards,

                                                                       Philip

-- 
Philip Lijnzaad, PhD
Holstege Genomics Laboratory
Dept. of Biomedical Genetics
University Medical Center (UMC), Utrecht
Stratenum room 2.211 (on Tuesdays and Thursdays not in after 15.00)
MSN chat (*NOT* email): philip_lijnzaad at hotmail.com
P.O. Box 85060, 3508 AB Utrecht
(Universiteitsweg 100, 3584 CG Utrecht)
The Netherlands
tel: +31 (0)8875 68464
fax: +31 (0)8875 68479

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