[BioC] Positive correlation between dye-swap technical replicates

[Naomi Altman]

I have seen positive correlation between dye-swaps due to dye degradation.

--Naomi

At 12:20 PM 2/3/2010, Philip Lijnzaad wrote:

> > 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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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111