From features to expression: High-density oligonucleotide array analysis revisited
Abstract
One of the most popular tools for large scale gene expression studies are high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20 small probe cells (``features'') for evaluating the transcript abundance of each gene. In addition, each probe is accompanied by a mismatched probe designed as a control for non-specificity. An algorithm is presented to compute comparative expression levels from the intensities of the individual features, based on a statistical study of their distribution. Interestingly, MM probes need not be included in the analysis. We show that our algorithm improves significantly upon the current standard and leads to a substantially larger number of genes brought above the noise floor for further analysis.
Keywords
Cite
@article{arxiv.physics/0102010,
title = {From features to expression: High-density oligonucleotide array analysis revisited},
author = {Felix Naef and Daniel A. Lim and Nila Patil and Marcelo O. Magnasco},
journal= {arXiv preprint arXiv:physics/0102010},
year = {2007}
}
Comments
9 pages, 7 figures