[BioC] The \"retain\" parameter in quality assessment of package PROcess

Yanqing [guest] guest at bioconductor.org
Mon Mar 24 16:14:36 CET 2014

I'm reading Chapter 6 of Gentleman et al.'s book. For the quality assessment of the 8 calibration spectra, the "retain" parameter has values 0.118-0.178 (on Page 102). The interpretation of "retain" is "the number of high peaks in a single spectrum". 

My question is, given the sparsity of peaks in a spectrum, how could the proportion of high peaks as large as above 10 percent?


 -- output of sessionInfo(): 

qualRes <- quality(M.r, peakfile, cutoff = 400)

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