[BioC] Cutoff selection for MassSpec

smohapat@vbi.vt.edu smohapat at vbi.vt.edu
Wed Dec 21 04:55:45 CET 2005


This refers to selection of cutoff for SELDI-TOF data as described in the
chapter 6 of Gentleman et al (Bioinformatics and Comp Bio Solutions using
R and Bioconductor).

On page 101 (Fig 6.5: cutpoint vs. average sd), the first local minimum
around 400 is chosen. However, in another dataset, page 106 (Fig 6.7) the
first local minimum around 350 is _not_ selected. Instead the chosen
cutoff 1000 is far too much to the right and not even on an local minimum.
I am unable to reconcile the two instances of cutoff choice.

Thanks for any explanation.


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