Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data

MOTIVATION Microarray experiments are affected by numerous sources of non-biological variation that contribute systematic bias to the resulting data. In a dual-label (two-color) cDNA or long-oligonucleotide microarray, these systematic biases are often manifested as an imbalance of measured fluorescent intensities corresponding to Sample A versus those corresponding to Sample B. Systematic bias...

cDNA Microarray Data Normalization

Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases.

Microarrays are often used to identify target genes that trigger specific diseases, to elucidate the mechanisms of drug effects, and to check SNPs. However, data from microarray experiments are well known to contain biases resulting from the experimental protocols. Therefore, in order to elucidate biological knowledge from the data, systematic biases arising from their protocols must be removed...

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...

Supplementary materials: Molecular analysis of positional identity in the developing mouse retina

The raw data from a cDNA microarray experiment consist of pairs of image files. Pre-processsing steps such as image anlysis and normalization are required to extract reliable measures of the fluorescence intensities and allowed comparisons within and between slides. All images were processed by Spot with foreground seeds set to 5 pixels square. In addition, within and between slide normalizatio...