A two-stage normalization method for partially degraded mRNA microarray data
Identifieur interne : 006311 ( Main/Exploration ); précédent : 006310; suivant : 006312A two-stage normalization method for partially degraded mRNA microarray data
Auteurs : Li-Yu D. Liu [Taïwan] ; Naisyin Wang [Taïwan, États-Unis] ; Joanne R. Lupton [États-Unis] ; Nancy D. Turner [États-Unis] ; Robert S. Chapkin [États-Unis] ; Laurie A. Davidson [États-Unis]Source :
- Bioinformatics [ 1367-4803 ] ; 2005-01.
English descriptors
- Teeft :
- Array, Baseline, Baseline array, Cdna microarray data, Central location, Codelink, Codelink arrays, Consecutive diet, Corresponding baseline intensities, Degraded, Density plots, Different arrays, Different proportions, Different treatment groups, Direct application, Empirical distribution function, Exfoliated colonocytes, False discovery rates, Fecal, Fecal array data, Fecal bioarray data, Fecal microarray data, Fecal samples, Fecal stream, Gene, Gene expression, Gene expression levels, Genetic information, Green line, Intensity levels, Invasive procedures, Large number, Local polynomial, Median, Microarray, Microarray dataset, Morphologically spots, Mrna, Mrna degradation, Normalization, Normalization methods, Normalization procedure, Normalization procedures, Outlying observations, Possible pairwise combinations, Probe, Proper normalization, Quantile, Quantile method, Quantile normalization, Quantile transformation, Robust inclusion step, Robustness consideration, Same array, Same distribution, Same treatment, Same treatment group, Scanning process, Scatter, Scatter plots, Second step, Simple step, Summary statistics, Total number, Treatment group, Treatment groups, Useful information.
Abstract
Motivation: The goal of the study is to obtain genetic information from exfoliated colonocytes in the fecal stream rather than directly from mucosa cells within the colon. The latter is obtained through invasive procedures. The difficulties encountered by this procedure are that certain probe information may be compromised due to partially degraded mRNA. Proper normalization is essential to obtaining useful information from these fecal array data. Results: We propose a new two-stage semiparametric normalization method motivated by the features observed in fecal microarray data. A location–scale transformation and a robust inclusion step were used to roughly align arrays within the same treatment. A non-parametric estimated non-linear transformation was then used to remove the potential intensity-based biases. We compared the performance of the new method in analyzing a fecal microarray dataset with those achieved by two existing normalization approaches: global median transformation and quantile normalization. The new method favorably compared with the global median and quantile normalization methods. Availability: The R codes implementing the two-stage method may be obtained from the corresponding author. Contact: nwang@stat.tamu.edu Supplementary information: Additional figures including scatter plots, MA plots and density plots of array differences may be found at http://stat.tamu.edu/~daisy/NSBRI/
Url:
DOI: 10.1093/bioinformatics/bti661
Affiliations:
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Davidson</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Nutrition and Food Science, Texas A&M University College Station, TX</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Environmental and Rural Health, Texas A&M University College Station, TX</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Bioinformatics</title><title level="j" type="abbrev">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2005-01">2005-01</date><biblScope unit="volume">21</biblScope><biblScope unit="issue">21</biblScope><biblScope unit="page" from="4000">4000</biblScope><biblScope unit="page" to="4006">4006</biblScope></imprint><idno type="ISSN">1367-4803</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1367-4803</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Array</term><term>Baseline</term><term>Baseline array</term><term>Cdna microarray data</term><term>Central location</term><term>Codelink</term><term>Codelink arrays</term><term>Consecutive diet</term><term>Corresponding baseline intensities</term><term>Degraded</term><term>Density plots</term><term>Different arrays</term><term>Different proportions</term><term>Different treatment groups</term><term>Direct application</term><term>Empirical distribution function</term><term>Exfoliated colonocytes</term><term>False discovery rates</term><term>Fecal</term><term>Fecal array data</term><term>Fecal bioarray data</term><term>Fecal microarray data</term><term>Fecal samples</term><term>Fecal stream</term><term>Gene</term><term>Gene expression</term><term>Gene expression levels</term><term>Genetic information</term><term>Green line</term><term>Intensity levels</term><term>Invasive procedures</term><term>Large number</term><term>Local polynomial</term><term>Median</term><term>Microarray</term><term>Microarray dataset</term><term>Morphologically spots</term><term>Mrna</term><term>Mrna degradation</term><term>Normalization</term><term>Normalization methods</term><term>Normalization procedure</term><term>Normalization procedures</term><term>Outlying observations</term><term>Possible pairwise combinations</term><term>Probe</term><term>Proper normalization</term><term>Quantile</term><term>Quantile method</term><term>Quantile normalization</term><term>Quantile transformation</term><term>Robust inclusion step</term><term>Robustness consideration</term><term>Same array</term><term>Same distribution</term><term>Same treatment</term><term>Same treatment group</term><term>Scanning process</term><term>Scatter</term><term>Scatter plots</term><term>Second step</term><term>Simple step</term><term>Summary statistics</term><term>Total number</term><term>Treatment group</term><term>Treatment groups</term><term>Useful information</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Motivation: The goal of the study is to obtain genetic information from exfoliated colonocytes in the fecal stream rather than directly from mucosa cells within the colon. The latter is obtained through invasive procedures. The difficulties encountered by this procedure are that certain probe information may be compromised due to partially degraded mRNA. Proper normalization is essential to obtaining useful information from these fecal array data. Results: We propose a new two-stage semiparametric normalization method motivated by the features observed in fecal microarray data. A location–scale transformation and a robust inclusion step were used to roughly align arrays within the same treatment. A non-parametric estimated non-linear transformation was then used to remove the potential intensity-based biases. We compared the performance of the new method in analyzing a fecal microarray dataset with those achieved by two existing normalization approaches: global median transformation and quantile normalization. The new method favorably compared with the global median and quantile normalization methods. Availability: The R codes implementing the two-stage method may be obtained from the corresponding author. Contact: nwang@stat.tamu.edu Supplementary information: Additional figures including scatter plots, MA plots and density plots of array differences may be found at http://stat.tamu.edu/~daisy/NSBRI/</div></front></TEI><affiliations><list><country><li>Taïwan</li><li>États-Unis</li></country><region><li>Texas</li></region></list><tree><country name="Taïwan"><noRegion><name sortKey="Liu, Li Yu D" sort="Liu, Li Yu D" uniqKey="Liu L" first="Li-Yu D." last="Liu">Li-Yu D. Liu</name></noRegion><name sortKey="Wang, Naisyin" sort="Wang, Naisyin" uniqKey="Wang N" first="Naisyin" last="Wang">Naisyin Wang</name></country><country name="États-Unis"><region name="Texas"><name sortKey="Wang, Naisyin" sort="Wang, Naisyin" uniqKey="Wang N" first="Naisyin" last="Wang">Naisyin Wang</name></region><name sortKey="Chapkin, Robert S" sort="Chapkin, Robert S" uniqKey="Chapkin R" first="Robert S." last="Chapkin">Robert S. Chapkin</name><name sortKey="Chapkin, Robert S" sort="Chapkin, Robert S" uniqKey="Chapkin R" first="Robert S." last="Chapkin">Robert S. Chapkin</name><name sortKey="Davidson, Laurie A" sort="Davidson, Laurie A" uniqKey="Davidson L" first="Laurie A." last="Davidson">Laurie A. Davidson</name><name sortKey="Davidson, Laurie A" sort="Davidson, Laurie A" uniqKey="Davidson L" first="Laurie A." last="Davidson">Laurie A. Davidson</name><name sortKey="Lupton, Joanne R" sort="Lupton, Joanne R" uniqKey="Lupton J" first="Joanne R." last="Lupton">Joanne R. Lupton</name><name sortKey="Lupton, Joanne R" sort="Lupton, Joanne R" uniqKey="Lupton J" first="Joanne R." last="Lupton">Joanne R. Lupton</name><name sortKey="Turner, Nancy D" sort="Turner, Nancy D" uniqKey="Turner N" first="Nancy D." last="Turner">Nancy D. Turner</name><name sortKey="Turner, Nancy D" sort="Turner, Nancy D" uniqKey="Turner N" first="Nancy D." last="Turner">Nancy D. Turner</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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