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Table 2 Double-bias-removal location normalization techniques used in this study. These strategies remove both spatial- and intensity effect either in a single step (IG SG LOESS) or in two steps (the remaining thirteen approaches) by combining methods listed in Table 1.

From: Evaluation of normalization methods for cDNA microarray data by k-NN classification

Name

Description: Method/Effect/Level

IG SG LOESS*

Joint Intensity/Global & Spatial/Global M l = M - lowess(A, rloc, cloc)

IG LOESS-SL LOESS

Step 1: IG LOESS/Intensity/Global lowess

Step 2: SL LOESS/Spatial/Local lowess

IL LOESS-SL LOESS

Step 1: IL LOESS/Intensity/Local lowess

Step 2: SL LOESS/Spatial/Local lowess

IG LOESS-SL FILTERW3

Step 1: IG LOESS/Intensity/Global lowess

Step 2: SL FILTERW3/Spatial/Local median filter

IG LOESS-SL FILTERW7

Step 1: IG LOESS/Intensity/Global lowess

Step 2: SL FILTERW7/Spatial/Local median filter

IST SPLINE-SL LOESS

Step 1: IST SPLINE/Intensity/Global spline

Step 2: SL LOESS/Spatial/Local lowess

IST SPLINE-SL FILTERW3

Step 1: IST SPLINE/Intensity/ Global spline

Step 2: SL FILTERW3/Spatial/Local median filter

IST SPLINE-SL FILTERW7

Step 1: IST SPLINE/Intensity/Global spline

Step 2: SL FILTERW7/Spatial/Local median filter

Q SPLINEG-SL LOESS

Step 1: Q SPLINEG/Intensity/Global qspline

Step 2: SL LOESS/Spatial/Local lowess

Q SPLINEG-SL FILTERW3

Step 1: Q SPLINEG/Intensity/Global qspline

Step 2: SL FILTERW3/Spatial/Local median filter

Q SPLINEG-SL FILTERW7

Step 1: Q SPLINEG/Intensity/Global qspline

Step 2: SL FILTERW7/Spatial/Local median filter

QS PLINER-SL LOESS

Step 1: QS PLINER/Intensity/Global qspline

Step 2: SL LOESS/Spatial/Local lowess

QS PLINER-SL FILTERW3

Step 1: QS PLINER/Intensity/Global qspline

Step 2: SL FILTERW3/Spatial/Local median filter

QS PLINER-SL FILTERW7

Step 1: QS PLINER/Intensity/Global qspline

Step 2: SL FILTERW7/Spatial/Local median filter

  1. * IG SG LOESS was implemented in the following package/function: MAANOVA R package/smooth (method="rlowess", f = 0.4, degree = 2). Elsewhere, IG SG LOESS is known as joint loess [21]. lowess(A, rloc, cloc): lowess curve fitted as a function of average log intensity (A), row location (rloc), and column location (cloc) of spots on a microarray.
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BMC Bioinformatics

ISSN: 1471-2105

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