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  Transcript normalization and segmentation of tiling array data

Zeller, G., Henz, S., Laubinger, S., Weigel, D., & Rätsch, G. (2008). Transcript normalization and segmentation of tiling array data. In Pacific Symposium on Biocomputing (PSB 2008) (pp. 527-538).

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Item Permalink: https://hdl.handle.net/21.11116/0000-000A-DE2E-A Version Permalink: https://hdl.handle.net/21.11116/0000-000A-DE32-4
Genre: Conference Paper

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http://psb.stanford.edu/psb-online/proceedings/psb08/ (Table of contents)
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 Creators:
Zeller, G1, Author           
Henz, SR, Author           
Laubinger, S, Author           
Weigel, D, Author           
Rätsch, G1, Author           
Affiliations:
1Rätsch Group, Friedrich Miescher Laboratory, Max Planck Society, ou_3378052              

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 Abstract: For the analysis of transcriptional tiling arrays we have developed two methods based on state-of-the-art machine learning algorithms. First, we present a novel transcript normalization technique to alleviate the effect of oligonucleotide probe sequences on hybridization intensity. It is specifically designed to decrease the variability observed for individual probes complementary to the same transcript. Applying this normalization technique to Arabidopsis tiling arrays, we are able to reduce sequence biases and also significantly improve separation in signal intensity between exonic and intronic/intergenic probes. Our second contribution is a method for transcript mapping. It extends an algorithm proposed for yeast tiling arrays to the more challenging task of spliced transcript identification. When evaluated on raw versus normalized intensities our method achieves highest prediction accuracy when segmentation is performed on transcript-normalized tiling array data.

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 Dates: 2008
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: PMID: 18229713
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Title: Pacific Symposium on Biocomputing (PSB 2008)
Place of Event: Fairmont Orchid, HI, USA
Start-/End Date: 2008-01-04 - 2008-01-08

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Title: Pacific Symposium on Biocomputing (PSB 2008)
Source Genre: Proceedings
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Publ. Info: -
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 527 - 538 Identifier: -