[BioC] how to annotate Illumina HumanHT-12 v3 chips?

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Mar 6 17:20:02 CET 2013


For sake of discussion/pedagogy, when you say:

> Sometimes you have to collapse the data to one probe per-gene, and for
> this I tend to pick the "best" probe for each gene by using a  measure
> such as IQR across the dataset.

In this scenario, which probe is "best" -- is it the one with the
largest IQR, or the smallest?

Assuming both probes map uniquely to the genome, both of which are (as
far as we know) "probing" the same gene of interest, what are some
"sound" reasons to pick one over the other?


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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