filterSpotsBySpikeIn: Filtering of spot values by the condition PM > MM and spot...

Description Usage Arguments Value

Description

Filtering of spot values by the condition PM > MM and spot intensity > spike in spot intensity

Usage

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filterSpotsBySpikeIn(MA, normMethod = "", subsetByManualControl = FALSE,
  subsetByPMvsMM = FALSE, ndups = 4, spacing = 1, weights = NULL,
  design, writeLog = TRUE)

Arguments

MA

MAList object as defined by limma

normMethod

Optional normalization method name that attached to the log file name (e.g. _vsn_)

subsetByManualControl

Boolean, data may be subsetted by the spike in controls

subsetByPMvsMMBoolean,

data may be subsetted by restriction PM > MM

ndups

Number of duplicated spots

spacing

Placement of the duplicated spots (in default mode it is assumed that spots are sorted)

weights

Parameter for avedups function

design

Design of the experiment is considered when caluclating restrictions (subsetByManualControl,subsetByPMvsMM)

writeLog

Writes a log file of the filtering steps

Value

Filtered MA object


SimonSchafferer/custom-neuro-ncRNA-microarray documentation built on May 9, 2019, 1:45 p.m.