[BioC] detection calls without MM probes

[Samuel Wuest]

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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