read_raw_public: Read Microarray data from GEO or ArrayExpress

In anschue/toxprofileR: Functions for Retrieving Dynamic Toxicogenomic Fingerprints

Description

Read Microarray data from GEO or ArrayExpress

Usage

read_raw_public(datadir, rawformat = c("Agilent", "Affymetrix",
  "Affymetrix_ST"), betweenArrayNorm = "cyclicloess", metadata,
  output = T, qc_coeff = c(ks = 3, sum = 3, iqr = 3, q = 3, d = 1),
  qc_sum = 1)

Arguments

datadir	data directory
rawformat	format of rawdatat (Agilen or Affymetrix)
betweenArrayNorm	name of normalization method
metadata	metadataframe
output	logical if output plot should be produced
qc_coeff	A named character vector giving the coefficient for acceptable intervals
qc_sum	Number of tests leading to array exclusion

Value

returns a normalized Elist

anschue/toxprofileR documentation built on Nov. 2, 2019, 1:55 p.m.