Genome-wide estimation of transcript concentrations from spotted cDNA microarray data

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data

A method providing absolute transcript concentrations from spotted microarray intensity data is presented. Number of transcripts per microg total RNA, mRNA or per cell, are obtained for each gene, enabling comparisons of transcript levels within and between tissues. The method is based on Bayesian statistical modelling incorporating available information about the experiment from target prepara...

Model-based estimation of transcript concentrations from spotted microarray data

Much data from spotted microarrays remain unused because obtained with different protocols, platforms or designs, making comparisons across experiments impossible. We have developed a model-based method, which provides absolute transcript levels. Transcript levels are universal, and can be included in further analyses with similar estimates obtained with different techniques in other laboratori...

cDNA Microarray Data Normalization

Spotted cDNA microarray image segmentation using ACWE

The segmentation of the picture (and, implicitly, the segmentation method used) is one of the three important steps in microarray image processing, together with spot gridding and information extraction. It directly affects the accuracy of gene expression analysis in the data mining process that follows. In 2001 a segmentation method for arbitrary pictures using the Active Contours Without Edge...

Predicting CpG Islands and DNA Methlation in the Cow Genome Using DNA Microarray Meta-Analysis and Genome Wide Scanning

DNA methylation is a type of epigenetic changes that directly affects DNA. In mammals, DNA methylation is essential for fetal development and stem cell differentiation and this phenomenon essentially occurs within the CpG islands. In this study, two methods were used to study the DNA methylation profile of cow genome. In the first method, the DNA methylation profile of the differentially expres...