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Semilinear high-dimensional model for normalization of microarray data: a theoretical analysis and partial consistency; Comment.

1. INTRODUCTION

I would like to begin by congratulating Fan, Peng, and Huang on their innovative approach to normalizing spotted cDNA microarray data. Although numerous articles have been written on this topic, the use of duplicate spots in the normalization process has rarely been discussed. Given the apparent within-slide spatial effects (Smyth, Yang, and Speed 2003; Balazsi, Kay, Barabasi, and Oltvai 2003), these spots have the potential to be very helpful not only in the normalization process itself, but also in assessing the effectiveness of a normalization procedure. Unfortunately, the focus of the article limits the discussion of this approach and leaves several ...

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