[BioC] Agilent Arrays

[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

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 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