Gustavo Fernández Bayón | 21 Nov 10:38 2012

Minfi preprocessing and rs probes

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?


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