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From features to expression: High-density oligonucleotide array analysis revisited

Felix Naef·Daniel A. Lim·Nila Patil·Marcelo O. Magnasco
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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.

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Felix Naef, Daniel A. Lim, Nila Patil, Marcelo O. Magnasco. 2001-02-21. From features to expression: High-density oligonucleotide array analysis revisited. https://arxiv.org/abs/physics/0102010

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