Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations

BMC Bioinformatics

Table 2 The properties of the normalization methods. MAS, Z, HK, Q, and WBL are sample-wise normalization and the gene-wise method AGC can be merged to each of them. This table lists the properties of each method.

	MAS	Z	HK	Q	WBL	AGC
Sample-wise normalization	Yes	Yes	Yes	Yes	Yes	No
Gene-wise normalization	No	No	No	No	No	Yes
Considers the array generation	No	No	No	No	Yes	Yes
Includes scaling	Yes	Yes	Yes	No	Yes	Yes
Based on distribution	No	No	No	Yes	Yes	No
May change the order of the values within a sample	No	No	No	No	No	Yes

ISSN: 1471-2105