[BioC] Dye bias adjustment of Illumina Infinium Methylation data

[Philip Lijnzaad]

On Tuesday 07 September 2010 19:17:14 Pan Du wrote:
> Hi Ina
>
> Based on our experience, dye bias does exist in most of our datasets, and
> the bias is usually consistent within the same batch. If all your data is
> in the same batch, then usually no color bias adjustment is necessary for
> Illumina Infinium methylation data. This is consistent with the Illumina
> explanation as you described. However, if your data includes several
> different batches, then dye bias adjustment is important if the dye bias is
> quite different across different batches.

We recently published a paper (Margaritis et al. 2009, Mol. Sys. Biol. 5:266; 
doi:10.1038/msb.2009.21) showing that 'local dye concentration' effects are 
responsible for dyebias in two-colour microarrays. If the sample is e.g. 
dUTP-labeled, both an increased A-content, increased melting temperature and 
an increased labeling percentage will increase the local dye concentration, 
and therefore increase the dye bias. The total dye bias therefore depends on 
both the hybridization and on the oligo-sequence. 

The Bioconductor package 'dyebias' contains code implementing the GASSCO 
method proposed in the paper, and really helps to reduce much of the dyebias. 

I don't know the details of the Illumina platform and protocols, but if the 
same premises apply, GASSCO should be able to address dyebias problems, also 
across different batches. I'd be interested to find out, so if you need help, 
feel free to contact me. 

Regards,
                                                                       Philip

-- 
Philip Lijnzaad, PhD
Holstege Genomics Laboratory
Dept. of Molecular Cancer Research
University Medical Center (UMC), Utrecht
Stratenum room 3.137 (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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