[BioC] Minfi preprocessing and rs probes

[Gustavo Fernández Bayón]

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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