Feature extraction and signal processing for nylon DNA microarrays.
Details
State: Public
Version: author
Serval ID
serval:BIB_30851
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Feature extraction and signal processing for nylon DNA microarrays.
Journal
BMC Genomics
ISSN
1471-2164
Publication state
Published
Issued date
2004
Volume
5
Number
1
Pages
38
Language
english
Notes
Publication types: Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
Abstract
BACKGROUND: High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels. RESULTS: We explore sources of variability in feature extraction from DNA microarrays on Nylon membrane with radioactive detection. We introduce a mathematical model of the signal emission and derive methods for correcting biases such as overshining, saturation or variation in probe amount. We also provide a quality metric which can be used qualitatively to flag weak or untrusted signals or quantitatively to modulate the weight of each experiment or gene in higher level analyses (clustering or discriminant analysis). CONCLUSIONS: Our novel feature extraction methodology, based on a mathematical model of the radioactive emission, reduces variability due to saturation, neighbourhood effects and variable probe amount. Furthermore, we provide a fully automatic feature extraction software, BZScan, which implements the algorithms described in this paper.
Keywords
Algorithms, Animals, Arabidopsis Proteins, Bias (Epidemiology), Breast Neoplasms, Carbon-Oxygen Ligases, Cluster Analysis, DNA, Neoplasm, DNA, Plant, Densitometry, Discriminant Analysis, Gene Expression Profiling, Humans, Image Processing, Computer-Assisted, Mice, Nylons, Oligonucleotide Array Sequence Analysis, Phosphorus Radioisotopes, Polymerase Chain Reaction, RNA, Messenger, Reproducibility of Results, Signal Processing, Computer-Assisted, Software
OAI-PMH
Pubmed
Web of science
Publisher's website
Open Access
Yes
Create date
19/11/2007 10:59
Last modification date
20/08/2019 14:15