[BioC] Minfi preprocessing and rs probes

[Gustavo Fernández Bayón]

Hi Kasper.  

It's perfectly clear for me now what rs* probes are. I should have read the Illumina guide before, I guess. But it is always a pleasure to ask in this list and learn a little bit more.

I agree with your decision about removing the probes. Problem is, GenomeStudio is calculating the betas for those probes too, which is something I think can lead to confusion. In my humble opinion, if something is not measuring methylation, showing a beta value for it on your interface is going to make a new user go mad (as has effectively happened to a fellow biologist in my lab).

I have another question. I was wondering about opening a new topic, but I think it might fit  in this context. Why is minfi not using the correction constant 100 in the denominator when calculating the betas? I have always wondered about that constant, because I did not see the exact reasoning behind it, and I am inclined to think more in your way o implementing it. In the end, it really makes no difference, doesn't it?

Regards,
Gus

---------------------------
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El miércoles 21 de noviembre de 2012 a las 17:35, Kasper Daniel Hansen escribió:

> The 'rs' probes are normal SNP probes; they do not measure
> methylation. Quoting from the Illumina methylation guide
> "rs# representsSNPassays (not affected by DNA methylation)"
> and
> "SNP assays can be used for sample identification and tracking. They
>   
> should be excluded for differential methylation analysis."

>  
> The purpose of these probes is for catching sample mix-ups. We have
> decided to remove them from the methylation object (MethylSet) because
> they do not measure methylation and the purpose of this object is to
> contain the methylation measurements.
>  
> Kasper
>  
>  
>  
>  
> On Wed, Nov 21, 2012 at 4:38 AM, Gustavo Fernández Bayón
> <gbayon at gmail.com (mailto:gbayon at gmail.com)> wrote:
> > Hi everybody.
> >  
> > I have just noticed that some probes disappeared during my workflow with minfi. When I looked into the preprocessing, I saw that preprocessIllumina() ends up calling preprocessRaw() in order to generate M and U signals. The interesting part is, only probes of type I and II are used for that. I noticed that the probes that were disappearing in my workflow are of type 'SNPI' and 'SNPII'.
> >  
> > Now I know in which part the probes are lost, but I would like to know the reason behind this procedure. Also, could anybody give me a hint if this is what Genomestudio is doing? What are this rs* probes useful for then?
> >  
> > Regards,
> > Gus
> >  
> >  
> >  
> > ---------------------------
> > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig)
> >  
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