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. 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