Some normalization methods assume that the two channels of intensities are related by a constant so that Microarray experiments allow RNA level measurements for many the center of the distribution of the log of the ratio is genes in multiple samples. However, mining the biological information shifted to zero. Chen et al. (1997) proposed an iterative from the large sets of data generated by micr...

PtGen2 is a 26,496 feature cDNA microarray containing amplified loblolly pine ESTs. The array is produced in our laboratory for use by researchers studying gene expression in pine and other conifer species. PtGen2 was developed as a result of our gene discovery efforts in loblolly pine, and is comprised of sequences identified primarily from root tissues, but also from needle and stem. PtGen2 h...

The biological materials available for cDNA microarray studies are often limiting. Thus, protocols have been developed to amplify RNAs isolated from limited amounts of tissues or cells. RNA amplification by in vitro transcription is the most widely used among the available amplification protocols. Two means of generating a dsDNA template for the RNA polymerase are a combination of reverse trans...

A vector processing based framework suitable for cDNA microarray image segmentation is introduced and analyzed in this paper. By using nonlinear, generalized selection vector filters the framework proposed here classifies the cDNA image data as either microarray spots or image background. The solution converges to a root signal that represents the segmented cDNA microarray image with the regula...

Microarray expression analysis has become one of the most widely used functional genomics tools. Efficient application of this technique requires the development of robust and reproducible protocols. We have optimized all aspects of the process, including PCR amplification of target cDNA clones, microarray printing, probe labeling and hybridization, and have developed strategies for data normal...

Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co-hybridized to every microarray. Often this reference consists of one experimental control sample, a pool of cell lines or a mix of all samples to be analyzed. We have developed an alternative common reference consisting of a mix of the products that are spotted on the array. Po...

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...

1689 www.drugdiscoverytoday.com The first attempts at global analysis of gene expression were undertaken in the mid-1970s with studies of the hybridization of an mRNA pool with radioactively labeled cDNA. Interest in gene expression increased steadily during the 1980s, and in the 1990s a new era of high throughput gene expression studies unfolded with the development of microarrays [1,2]. Altho...

UNLABELLED The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA m...