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Table 1 Calibration options within Affy

From: Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips

Calibration step

Option 1

Option 2

Option 3

Option 4

Option 5

Background subtraction

Nothing

RMA

MAS

  

Normalisation

Constant

Invariant set

Lowess

Qspline

Quantiles

Expression Measure

Li-Wong (MBEI)

Median Polish (RMA)

MAS5

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