dorsal/arxiv
View SchemaFrom features to expression: High-density oligonucleotide array analysis revisited
| Authors | Felix Naef, Daniel A. Lim, Nila Patil, Marcelo O. Magnasco |
|---|---|
| Categories | |
| ArXiv ID | physics/0102010 |
| URL | https://arxiv.org/abs/physics/0102010 |
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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"abstract": "One of the most popular tools for large scale gene expression studies are\nhigh-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20\nsmall probe cells (``features\u0027\u0027) for evaluating the transcript abundance of\neach gene. In addition, each probe is accompanied by a mismatched probe\ndesigned as a control for non-specificity. An algorithm is presented to compute\ncomparative expression levels from the intensities of the individual features,\nbased on a statistical study of their distribution. Interestingly, MM probes\nneed not be included in the analysis. We show that our algorithm improves\nsignificantly upon the current standard and leads to a substantially larger\nnumber of genes brought above the noise floor for further analysis.",
"arxiv_id": "physics/0102010",
"authors": [
"Felix Naef",
"Daniel A. Lim",
"Nila Patil",
"Marcelo O. Magnasco"
],
"categories": [
"physics.bio-ph",
"physics.data-an",
"q-bio"
],
"title": "From features to expression: High-density oligonucleotide array analysis revisited",
"url": "https://arxiv.org/abs/physics/0102010"
},
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