[BioC] Minfi preprocessing and rs probes

[Kasper Daniel Hansen]

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> 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
>
>
>
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