Entering edit mode
My experience is that Agilent arrays respond to the same analysis
methods
as do other two colour arrays, apart from using global loess instead
of
print-tip loess normalisation. The generally high quality just means
that
you get more benefit from the analysis. We have found for example that
accommodating dye-effects into the linear model particularly important
for
Agilent arrays. You might well have more confidence in analysing the
red
and green channels individually for Agilent arrays, but this is not
the
same as treating the arrays as two one-channel arrays. See for example
lmscFit() in the limma package.
Gordon
>Claus Mayer claus at bioss.ac.uk
>Wed Jun 22 19:18:19 CEST 2005
>
>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