Julien,
There are indeed alternatives to the MAS5 present/absent call method,
but
only with some limitations:
a) Half-Price method, please refer to Wu et al, 2005 (see below). The
method
is using only PM probe signals, but you will have to ask the authors
for the
script, there is no package available for the tool; or,
alternaltively, make
your own with the idea that the authors mention...
b) PANP ? present/absent calls with negative probesets, please refer
to
Warren et al (2007), or the Bioconductor package PANP
The method is only
available for the Affymetrix HG-U133 series, but personally, I have
modified
it for the Arabidopsis ATH1 array and it performs very well on my
data...
PANP can be used with different preprocessing methods of your choice,
but
everything is nicely described in the reference.
Beside that, there is no alternative that I would know of, but maybe
other
from the list would have suggestions?
Best, Sam
References:
Zhijin Wu and Rafael A. Irizarry, "A Statistical Framework for the
Analysis
of Microarray Probe-Level Data" (March 2005). Johns Hopkins
University,
Dept. of Biostatistics Working Papers. Working Paper 73.
http://www.bepress.com/jhubiostat/paper73
Warren, P., Bienkowska, J., Martini, P., Jackson, J., and Taylor, D.,
PANP -
a New
Method of Gene Detection on Oligonucleotide Expression Arrays (2007),
under
review, www.people.brandeis.edu/~dtaylor/Taylor_Papers/BIBE07_PANP.pdf
or the Bioconductor Vignette for the PANP package
www.bioconductor.org)
------------------------------------------------------
Wuest Samuel
Smurfit Institute of Genetics
Trinity College Dublin
Dublin 2, Ireland
Phone: +353-1-896 2444
Mobile: + 353-85-735 5821
Email: wuests at tcd.ie
------------------------------------------------------
On Fri, 14 Mar 2008 14:11:17 +0100
Julien Roux <julien.roux at="" unil.ch=""> wrote:
> Hi list,
>
> When using MAS5 detection calls in affymetrix chips, the assumption
is
> that the MM probes give a reasonable estimate of background. If we
> normalize affy chips with RMA, MM probes are not used.
> In similar way, I was wondering if another method was available to
> estimate the presence/absence of genes without teh use of MM probes?
>
> I think this would be feasible since RMA estimates the parameters of
the
> background distribution (bg.parameters), I just don't really know
how to
> handle this...
> Thanks a lot for your help
> Julien
>
> --
> Julien Roux, PhD student
>
http://www.unil.ch/dee/page22707.html
> Department of Ecology and Evolution
> Biophore, University of Lausanne, 1015 Lausanne, Switzerland
> tel: +41 21 692 4221 fax: +41 21 692 4165
>
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