Non-linear Normalization and Background Correction in One-channel CDNA Microarray Studies

cDNA Microarray Data Normalization

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...

Effect of Background Correction on Cancer Classification with Gene Expression Data

This paper empirically compares six background correction methods aimed at removing unspecific background noise of the overall signal level measured by a scanner across microarrays. Using three published cDNA microarray datasets we investigated the effect of background correction on cancer classification in terms of the predictive performance of two classifiers (k-NN and support vector machine ...

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.

We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and tha...

A Two-Way Semi-Linear Model for Normalization and Significant Analysis of cDNA Microarray Data

A basic question in analyzing cDNA microarray data is normalization. The purpose of normalization is to remove systematic bias in the observed expression values by establishing a normalization curve across the whole dynamic range. A proper normalization procedure ensures that the normalized intensity ratios provide meaningful measures of relative expression levels. We propose a two-way semi-lin...