lmdme: Linear Models on Designed Multivariate Experiments in R
- Autores
- Fresno Rodríguez, Cristóbal; Balzarini, Monica Graciela; Fernandez, Elmer Andres
- Año de publicación
- 2014
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Thelmdmepackage decomposes analysis of variance (ANOVA) through linear mod-els on designed multivariate experiments, allowing ANOVA-principal component analysis(APCA) and ANOVA-simultaneous component analysis (ASCA) inR. It also extends bothmethods with the application of partial least squares (PLS) through the specification ofa desired output matrix. The package is freely available fromBioconductorand licensedunder the GNU General Public License.ANOVA decomposition methods for designed multivariate experiments are becomingpopular in “omics” experiments (transcriptomics, metabolomics, etc.), where measure-ments are performed according to a predefined experimental design, with several exper-imental factors or including subject-specific clinical covariates, such as those present incurrent clinical genomic studies. ANOVA-PCA and ASCA are well-suited methods forstudying interaction patterns on multidimensional datasets. However, currently anRimplementation of APCA is only available forSpectradata in theChemoSpecpackage,whereas ASCA is based on average calculations on the indices of up to three design ma-trices. Thus, no statistical inference on estimated effects is provided. Moreover, ASCA isnot available in anRpackage.Here, we present anRimplementation for ANOVA decomposition with PCA/PLSanalysis that allows the user to specify (through a flexibleformulainterface), almostany linear model with the associated inference on the estimated effects, as well as todisplay functions to explore results both of PCA and PLS. We describe the model, itsimplementation and two high-throughputmicroarrayexamples: one applied to interactionpattern analysis and the other to quality assessment.
Fil: Fresno Rodríguez, Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Católica de Córdoba; Argentina
Fil: Balzarini, Monica Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba; Argentina
Fil: Fernandez, Elmer Andres. Universidad Católica de Córdoba; Argentina - Materia
-
LINEAR MODEL
ANOVA DESCOMPOSITION
PCA
PLS
DESIGNED EXPERIMENTS
R - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/33951
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lmdme: Linear Models on Designed Multivariate Experiments in RFresno Rodríguez, CristóbalBalzarini, Monica GracielaFernandez, Elmer AndresLINEAR MODELANOVA DESCOMPOSITIONPCAPLSDESIGNED EXPERIMENTSRhttps://purl.org/becyt/ford/1.1https://purl.org/becyt/ford/1Thelmdmepackage decomposes analysis of variance (ANOVA) through linear mod-els on designed multivariate experiments, allowing ANOVA-principal component analysis(APCA) and ANOVA-simultaneous component analysis (ASCA) inR. It also extends bothmethods with the application of partial least squares (PLS) through the specification ofa desired output matrix. The package is freely available fromBioconductorand licensedunder the GNU General Public License.ANOVA decomposition methods for designed multivariate experiments are becomingpopular in “omics” experiments (transcriptomics, metabolomics, etc.), where measure-ments are performed according to a predefined experimental design, with several exper-imental factors or including subject-specific clinical covariates, such as those present incurrent clinical genomic studies. ANOVA-PCA and ASCA are well-suited methods forstudying interaction patterns on multidimensional datasets. However, currently anRimplementation of APCA is only available forSpectradata in theChemoSpecpackage,whereas ASCA is based on average calculations on the indices of up to three design ma-trices. Thus, no statistical inference on estimated effects is provided. Moreover, ASCA isnot available in anRpackage.Here, we present anRimplementation for ANOVA decomposition with PCA/PLSanalysis that allows the user to specify (through a flexibleformulainterface), almostany linear model with the associated inference on the estimated effects, as well as todisplay functions to explore results both of PCA and PLS. We describe the model, itsimplementation and two high-throughputmicroarrayexamples: one applied to interactionpattern analysis and the other to quality assessment.Fil: Fresno Rodríguez, Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Católica de Córdoba; ArgentinaFil: Balzarini, Monica Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Fernandez, Elmer Andres. Universidad Católica de Córdoba; ArgentinaJournal Statistical Software2014-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/33951Fresno Rodríguez, Cristóbal; Balzarini, Monica Graciela; Fernandez, Elmer Andres; lmdme: Linear Models on Designed Multivariate Experiments in R; Journal Statistical Software; Journal Of Statistical Software; 56; 7; 4-2014; 1-161548-7660CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.jstatsoft.org/article/view/v056i07info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:43:17Zoai:ri.conicet.gov.ar:11336/33951instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:43:17.689CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
lmdme: Linear Models on Designed Multivariate Experiments in R |
title |
lmdme: Linear Models on Designed Multivariate Experiments in R |
spellingShingle |
lmdme: Linear Models on Designed Multivariate Experiments in R Fresno Rodríguez, Cristóbal LINEAR MODEL ANOVA DESCOMPOSITION PCA PLS DESIGNED EXPERIMENTS R |
title_short |
lmdme: Linear Models on Designed Multivariate Experiments in R |
title_full |
lmdme: Linear Models on Designed Multivariate Experiments in R |
title_fullStr |
lmdme: Linear Models on Designed Multivariate Experiments in R |
title_full_unstemmed |
lmdme: Linear Models on Designed Multivariate Experiments in R |
title_sort |
lmdme: Linear Models on Designed Multivariate Experiments in R |
dc.creator.none.fl_str_mv |
Fresno Rodríguez, Cristóbal Balzarini, Monica Graciela Fernandez, Elmer Andres |
author |
Fresno Rodríguez, Cristóbal |
author_facet |
Fresno Rodríguez, Cristóbal Balzarini, Monica Graciela Fernandez, Elmer Andres |
author_role |
author |
author2 |
Balzarini, Monica Graciela Fernandez, Elmer Andres |
author2_role |
author author |
dc.subject.none.fl_str_mv |
LINEAR MODEL ANOVA DESCOMPOSITION PCA PLS DESIGNED EXPERIMENTS R |
topic |
LINEAR MODEL ANOVA DESCOMPOSITION PCA PLS DESIGNED EXPERIMENTS R |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.1 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Thelmdmepackage decomposes analysis of variance (ANOVA) through linear mod-els on designed multivariate experiments, allowing ANOVA-principal component analysis(APCA) and ANOVA-simultaneous component analysis (ASCA) inR. It also extends bothmethods with the application of partial least squares (PLS) through the specification ofa desired output matrix. The package is freely available fromBioconductorand licensedunder the GNU General Public License.ANOVA decomposition methods for designed multivariate experiments are becomingpopular in “omics” experiments (transcriptomics, metabolomics, etc.), where measure-ments are performed according to a predefined experimental design, with several exper-imental factors or including subject-specific clinical covariates, such as those present incurrent clinical genomic studies. ANOVA-PCA and ASCA are well-suited methods forstudying interaction patterns on multidimensional datasets. However, currently anRimplementation of APCA is only available forSpectradata in theChemoSpecpackage,whereas ASCA is based on average calculations on the indices of up to three design ma-trices. Thus, no statistical inference on estimated effects is provided. Moreover, ASCA isnot available in anRpackage.Here, we present anRimplementation for ANOVA decomposition with PCA/PLSanalysis that allows the user to specify (through a flexibleformulainterface), almostany linear model with the associated inference on the estimated effects, as well as todisplay functions to explore results both of PCA and PLS. We describe the model, itsimplementation and two high-throughputmicroarrayexamples: one applied to interactionpattern analysis and the other to quality assessment. Fil: Fresno Rodríguez, Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Católica de Córdoba; Argentina Fil: Balzarini, Monica Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba; Argentina Fil: Fernandez, Elmer Andres. Universidad Católica de Córdoba; Argentina |
description |
Thelmdmepackage decomposes analysis of variance (ANOVA) through linear mod-els on designed multivariate experiments, allowing ANOVA-principal component analysis(APCA) and ANOVA-simultaneous component analysis (ASCA) inR. It also extends bothmethods with the application of partial least squares (PLS) through the specification ofa desired output matrix. The package is freely available fromBioconductorand licensedunder the GNU General Public License.ANOVA decomposition methods for designed multivariate experiments are becomingpopular in “omics” experiments (transcriptomics, metabolomics, etc.), where measure-ments are performed according to a predefined experimental design, with several exper-imental factors or including subject-specific clinical covariates, such as those present incurrent clinical genomic studies. ANOVA-PCA and ASCA are well-suited methods forstudying interaction patterns on multidimensional datasets. However, currently anRimplementation of APCA is only available forSpectradata in theChemoSpecpackage,whereas ASCA is based on average calculations on the indices of up to three design ma-trices. Thus, no statistical inference on estimated effects is provided. Moreover, ASCA isnot available in anRpackage.Here, we present anRimplementation for ANOVA decomposition with PCA/PLSanalysis that allows the user to specify (through a flexibleformulainterface), almostany linear model with the associated inference on the estimated effects, as well as todisplay functions to explore results both of PCA and PLS. We describe the model, itsimplementation and two high-throughputmicroarrayexamples: one applied to interactionpattern analysis and the other to quality assessment. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-04 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/33951 Fresno Rodríguez, Cristóbal; Balzarini, Monica Graciela; Fernandez, Elmer Andres; lmdme: Linear Models on Designed Multivariate Experiments in R; Journal Statistical Software; Journal Of Statistical Software; 56; 7; 4-2014; 1-16 1548-7660 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/33951 |
identifier_str_mv |
Fresno Rodríguez, Cristóbal; Balzarini, Monica Graciela; Fernandez, Elmer Andres; lmdme: Linear Models on Designed Multivariate Experiments in R; Journal Statistical Software; Journal Of Statistical Software; 56; 7; 4-2014; 1-16 1548-7660 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://www.jstatsoft.org/article/view/v056i07 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Journal Statistical Software |
publisher.none.fl_str_mv |
Journal Statistical Software |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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13.070432 |