Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates

DOI10.1016/J.COMPBIOLCHEM.2007.02.008MaRDI QIDQ2373294zbMATH OpenOpenAlexWikidataFDO

Authors Raad Z. Gharaibeh, Anthony A. Fodor, Cynthia J. Gibas

Publication date 17 July 2007

Published in Computational Biology and Chemistry (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc2043163

zbMATH Keywords

DNA microarrayBackground correctionProbe secondary structure

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Recommendations

• A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
• Exploration, normalization, and summaries of high density oligonucleotide array probe level data
• Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
• Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
• A systematic statistical linear modeling approach to oligonucleotide array experiments

Cites work

• Effects of DNA secondary structure on oligonucleotide probe binding efficiency
• Exploration, normalization, and summaries of high density oligonucleotide array probe level data
• Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection

Cited in

(5)

• The detection of blur in Affymetrix GeneChips
• A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
• Effects of DNA secondary structure on oligonucleotide probe binding efficiency
• Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
• Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays

Describes a project that uses

Uses Software

• DINAMelt
• Sfold
• affypdnn

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