affy.Microarray.preprocessing: internal fxn for affymatrix IVT microarray preprocessing

In htc502/ewrefxn: this package collects r fxns useful in my daily coding life

Description

internal fxn for affymatrix IVT microarray preprocessing

Usage

affy.Microarray.preprocessing(
  phenoData,
  Preprocessing = "mas5",
  PMA_cutoff = 0.1,
  auto.annot = T,
  symbol = F,
  ann.file = NULL,
  ann.col = 13,
  multiple2one = "Variance"
)

Arguments

phenoData	a table derived from sdrf file which must have two columns called ArrayDataFile and State
Preprocessing	prep method to use, possible values: mas5, dchip, rma, gcrma
PMA_cutoff	percentage threshold of samples which failed the PMA calling test
auto.annot	set to TURE for automatically annotation of the probes
symbol	set to TURE to get gene symbol annotation instead of entrezID
ann.file	if auto.annot = F, this file will be used to annote the probes
ann.col	if auto.annot = F, this column of the ann.file will be used to annote the probes
multiple2one	method for merge the probes corresponding to the same gene

Value

an expressionSet object

Author(s)

dapeng, liang and guangchun, han

htc502/ewrefxn documentation built on Feb. 2, 2020, 9:14 a.m.