preprocessed: Standard NOWAC preprocessing

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

Description

Performs the standard NOWAC preprocessing steps on your data. This happens after outlier removal. Performs the following steps in the following order:

• Background correction. Uses negative control probes (probes that are designed to detect noise) to do a normal-exponential convolution correction

• Normalization. Quantile/shoehorn normalization.

• Probe filtering. Filters out porobes with bad annotation quality, probes below detection threshold, and probes that arent' present in a certain fraction of the population.

• Probe aggregation. Combine probes that detect the same gene to a single value.

Usage

preprocessed(data, negative_controls, pval = 0.01, fval = 0.01,
  verbose = FALSE)

Arguments

data	matrix or LumiBatch, observations by columns, probes by rows
negative_controls	matrix of negative probe intensities for background correction.
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 extra info about filtering/aggregation of probes? Defaults to no.

Value

a processed object of same type as data

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