New normalization methods for cDNA microarray data

cDNA Microarray Data Normalization

New Normalization Methods for CDNA Microarray Data

MOTIVATION The focus of this paper is on two new normalization methods for cDNA microarrays. After the image analysis has been performed on a microarray and before differentially expressed genes can be detected, some form of normalization must be applied to the microarrays. Normalization removes biases towards one or other of the fluorescent dyes used to label each mRNA sample allowing for prop...

Normalization of cDNA microarray data.

Normalization means to adjust microarray data for effects which arise from variation in the technology rather than from biological differences between the RNA samples or between the printed probes. This paper describes normalization methods based on the fact that dye balance typically varies with spot intensity and with spatial position on the array. Print-tip loess normalization provides a wel...

A new outlier removal approach for cDNA microarray normalization.

Normalization is a critical step in the analysis of microarray gene expression data. For dual-labeled array, traditional normalization methods assume that the majority of genes are non-differentially expressed and that the number of overexpressed genes approximately equals the number of under-expressed genes. However, these assumptions are inappropriate in some particular conditions. Differenti...

Identification and Normalization of Plate Effects in Cdna Microarray Data

Introducing a new way of visualizing cDNA microarray data we have identified a new type of systematic variation, which we refer to as plate effects. We believe that plate effects are due to non-biological differences in the cDNA clones products spotted onto the microarray slides. By comparing the consistency of all replicates (both within and between slides) after performing 42 different normal...