. Author manuscript; available in PMC: 2019 Nov 4.

Published in final edited form as: Regul Toxicol Pharmacol. 2017 Nov 4;91(Suppl 1):S36–S45. doi: 10.1016/j.yrtph.2017.11.001

Table 1:

Specification of the raw data and the normalisation method taking the examples of Agilent and Affymetrix microarray platforms

	Agilent microarray platforms	Affymetrix microarray platforms
Specification of the raw data
Images of signal intensities	If applicable	Yes
Raw data	Specification if median, mean or processed signal intensity was used as the raw data
Quantification	Specification of feature extraction tool	Generally: Affymetrix software
Data files	TXT	CEL
Background subtraction	If applicable; and including background measured
Specification of the normalisation method
	Two colour (locally weighted scatterplot smoothing (LOWESS) normalisation; options include span, degree, etc.) or one colour (quantile, cyclic LOWESS, variance stabilisation normalisation (VSN), etc.)	e.g., robust multi-array average (RMA), MicroArray Suite (MAS), version 5.0, etc. Specification if data were adjusted for confounders before or after normalisation