Dear Jim and Steve, 

Many thanks for your answers and for your tips. I´ve learn a lot and I´ll try to tell all this information to my supervisor. 

Many thanks again 

Juan 

--------------------------------------------------------------- 
Juan Fernandez Tajes, ph. D 
Grupo XENOMAR 
Departamento de Biología Celular y Molecular 
Facultad de Ciencias-Universidade da Coruña 
Tlf. +34 981 167000 ext 2030 
e-mail: jfernandezt@udc.es 
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De: "Steve Lianoglou" <mailinglist.honeypot@gmail.com> 
Para: "James W. MacDonald" <jmacdon@uw.edu> 
CC: "Juan Fernández Tajes" <jfernandezt@udc.es>, "bioconductor" <bioconductor@r-project.org> 
Enviados: Viernes, 28 de Septiembre 2012 17:41:31 
Asunto: Re: [BioC] Analyzing expression Affymetrix Hugene1.0.st array 

Hi, 

Totally agree w/ everything Jim has said (this is usually a smart 
thing to do), but just wanted to comment on: 
On Fri, Sep 28, 2012 at 11:21 AM, James W. MacDonald <jmacdon@uw.edu> wrote: 
[snip] 

> I think this becomes a bit more difficult with the Gene ST arrays, as the
> negative controls have a nasty habit of looking not only expressed, but 
> differentially expressed. A lot of these controls are supposed to target
> introns, which makes me wonder how much of the total RNA extracted from a
> cell is mRNA for which the introns have yet to be excised. 

Instead of such negative control probes, perhaps you (Juan) might know 
something about the types of cells you have data from. In particular, 
perhaps you can justify identifying a multitude of genes that you know 
not to be expressed in these cell types and use some statistics over 
their probe expression to rig up a lower bound of your detection 
limit. 

If you don't know this info, and have no expert to ask, maybe you can 
find rna-seq data in cells "close" (using some definition of "close" 
that makes you comfortable) and use that to find such non-transcribed 
genes. 

I guess there's also going to probe (sequence content) effects that 
affect the expression readout of these "silent" probes and what not, 
but ... if you're going for some heuristic thing that you're not using 
as the lynchpin of your study, then perhaps this is passable. 

-steve 

-- 
Steve Lianoglou 
Graduate Student: Computational Systems Biology 
| Memorial Sloan-Kettering Cancer Center 
| Weill Medical College of Cornell University 
Contact Info: http://cbio.mskcc.org/~lianos/contact 

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