[BioC] Agilent Arrays

[Wolfgang Huber]

Hi Claus,

for the normalization of arrays where the spotting etc. variability
between chips is not strong, you can treat the data from m two-colour
arrays as if it were 2*m single colour ones, and use methods like
"quantiles" or "vsn".

Note that for almost all genes, the hybridization is not limited by the
amount of probe DNA, hence the competition between red and gree target is
negligible for almost all genes (execept possibly the most highly
expressed ones). This justifies treating a two-color array like two
single-color arrays.

Only later when you consider the contrasts of interest for finding
differentially expressed genes, you want to make sure that these are not
confounded with dye.

PS, I think your question is very directly Bioconductor related!

Best wishes
  Wolfgang


<quote who="Claus Mayer">
> Dear all!
>
> Apologies for asking a question which is not directly Bioconductor
> related: After some experience with spotted 2-channel arrays and
> Affydata, I am currently analysing my first data set based on Agilent
> arrays. I know that packages like marray or limma have facilities to
> read these data and that they can be normalised and analysed like any
> other 2-colour-arrays. On the other hand the printing technology of
> these arrays (using inkjet-printing of 60mer oligos) is closer in spirit
> to Affy, if I understand this correctly. This seems to show in the data
> as well. For example the strongest correlations I found in the single
> channel (log-)intensities was not between the two channels observed on
> the same slide (like with spotted arrays), but between the two channels
> (differently dyed on different arrays in a loop design) that contained
> the same sample (which is quite reassuring). This made me wonder whether
> (once dye and array effects have been removed by some normalisation
> method) with Agilent arrays one might really use single channel
> intensities as measures of gene expression instead of reducing them to
> the log-ratio only as is usually done for two-channel data.
>
> This would have consequences on the way these arrays should be
> normalised (rather by a multichip method than individually) and also
> allow more flexibility in the design of experiments.
>
> As I said before this is my first Agilent data set, so I would be
> interested to hear opinions of others with more experience. Before I
> start to re-invent the wheel here, I’d be also interested to know
> whether any of you is aware of tools, software, papers, etc
 dealing
> with the analysis of Agilent array data specifically (rather than just
> applying standard methods for 2-coloured cDNA -arrays).
>
> Any help/comments appreciated
>
> Claus
>
> --
> ***********************************************************************************
>  Claus-D. Mayer                       | http://www.bioss.ac.uk
>  Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
>  Rowett Research Institute            | Telephone: +44 (0) 1224 716652
>  Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349
>
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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