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Assessing statistical significance in microarray experiments using the distance between microarrays.

Hayden D, Lazar P, Schoenfeld D, Inflammation and the Host Response to Injury Investigato - PLoS ONE (2009)

Bottom Line: We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations.For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis.The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data.

View Article: PubMed Central - PubMed

Affiliation: Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America. dhayden@partners.org

ABSTRACT
We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations. For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis. The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data. An R software package, permtest, implementing the method is freely available from the Comprehensive R Archive Network at http://cran.r-project.org.

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Related in: MedlinePlus

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pone-0005838-g001: Heat Map

Mentions: Figure 1 shows a heat map of day one gene expression for the 48 patients (columns) over the 445 probesets (rows). In the figure, columns labeled with a “1” comprise the early recovery group, those labeled with a “2” comprise the late recovery group. Hierarchical clustering using Euclidean distance has been applied to the patients but not the probesets.


Assessing statistical significance in microarray experiments using the distance between microarrays.

Hayden D, Lazar P, Schoenfeld D, Inflammation and the Host Response to Injury Investigato - PLoS ONE (2009)

Heat Map
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2691999&req=5

pone-0005838-g001: Heat Map
Mentions: Figure 1 shows a heat map of day one gene expression for the 48 patients (columns) over the 445 probesets (rows). In the figure, columns labeled with a “1” comprise the early recovery group, those labeled with a “2” comprise the late recovery group. Hierarchical clustering using Euclidean distance has been applied to the patients but not the probesets.

Bottom Line: We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations.For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis.The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data.

View Article: PubMed Central - PubMed

Affiliation: Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America. dhayden@partners.org

ABSTRACT
We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations. For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis. The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data. An R software package, permtest, implementing the method is freely available from the Comprehensive R Archive Network at http://cran.r-project.org.

Show MeSH
Related in: MedlinePlus