filtered: Filtering of bad quality/non-detectable probes

In 3inar/nowaclean: Methods for Standardized Data Cleaning in the Norwegian Women and Cancer Group

Description

Filters out probes that have a signal below a specified detection threshold and that arent expressed in at least some specified fraction of observations. Also removes probes of "poor" or "no match" quality. See reference

Usage

filtered(data, pval = 0.01, fval = 0.01, verbose = FALSE)

Arguments

data	a LumiBatch
pval	a threshold for non-detection of a signal. a signal with detection p-value above pval will be discarded.
fval	the smallest proportion of observations in which a signal should be detected (as defined by pval). If fval is 0.5, there must be a detectable signal in half the observations or the probe will be discarded.
verbose	print info about filtered-out probes? T/F

References

Günther C, Holden M, Holden L. Preprocessing of gene-expression data related to breast cancer diagnosis: SAMBA/35/14. https://www.nr.no/files/samba/smbi/note2015SAMBA3514preprocessing.pdf

3inar/nowaclean documentation built on May 5, 2019, 10:44 a.m.