[BioC] Limma and spot-specific dye effects for an environmental microarray

[Philip Lijnzaad]

On Friday 24 June 2011 02:07:36 Ross Chapman wrote:

>  Is there a way
> to remove the spot*dye effect from the normalised data from individual
> arrays so I can make an equal comparison of values from all samples
> using, for a heatmap for example, without dye effects confounding the
> result.

Dear Ross,

a while ago we published a method, GASSCO (see below), that gets rid of 
gene-specific (or more precisely, probe sequence-specific) dye bias. This 
bias is visible as an influence of the dye orientation on the signals, and 
differs between probes but also between hybridizations. The artefact cannot 
be corrected by ordinary normalization methods such as LOESS, nor by using 
e.g. anova, since it  is roughly the product of a probe-specific part 
(correlated to the A-content, when using dUTP labeling) and a 
hybridization-specific part (roughly linear with the labeling percentage).

The GASSCO method is implemented in the Bioconductor package 'dyebias'; it may 
help you establish whether there is any gene-specific dye bias present, and 
lets you get rid of it. Let me know if you need any help with it. 

                                                                      Philip



Margaritis et al. (2009) Adaptable gene-specific dye bias correction for 
two-channel DNA microarrays. Mol. Sys. Biol. 5, 266.

-- 
Philip Lijnzaad, PhD
Molecular Cancer Research
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

------------------------------------------------------------------------------

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

------------------------------------------------------------------------------

This message may contain confidential information and is...{{dropped:8}}