[BioC] single-array error model

[Wolfgang Huber]

Hi Francoise,

are you aware of a sufficiently detailed description of that error model,
which would allow to estimate its parameters from data?

I think that the additive-multiplikative error model by Blythe Durbin and
David Rocke is related to that of Hughes et al.: Rocke DM, Durbin B. A
model for measurement error for gene expression arrays. J Comput Biol.
2001;8(6):557-69.
PMID: 11747612

But I would be happy to be corrected if I am wrong.

The Rocke-Durbin model is used in the package "vsn" for the estimation of
background correction and normalization parameters, and can be used to
derive attenuated log-ratios that have intensity-independent variance. See
also: http://www.bepress.com/bioconductor/paper6

Best regards
 Wolfgang

<quote who="Thibaud-Nissen, Francoise">
> Hi,
>
>
>
> Has anybody used the single-array error model described in the
> supplemental material of Hughes et al., Cell, 102, 109 (2000)? It models
> uncertainties in individual arrays, and is widely used in ChIP-chip
> analysis.
>
>
>
> I would like to know if anybody has used it and liked it and if it is
> implemented in R.
>
>
>
> This method was also used in
>
> Ren et al., Science (2000), 290, 2306
>
> Lee et al. Science (2002), 298, 799
>
> Li et al., PNAS (2003), 100, 8164
>
> ...
>
>
>
> Thanks,
>
>
>
> Françoise Thibaud-Nissen
>
>
> 	[[alternative HTML version deleted]]
>
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>


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.ebi.ac.uk/huber