Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject for permutation tests. Best regards João Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers Allé 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: Joao.Fadista@agrsci.dk <mailto:Joao.Fadista@agrsci.dk> Web: agrsci.org <agrsci.org> ________________________________ DJF now offers new degree programmes <agrsci.org/content/view/full/34133> . News and news media <agrsci.org/navigation/nyheder_og_presse> . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]]
Dear Jo?o, You can do permutation tests on an unbalanced design. HTH, Thierry ---------------------------------------------------------------------------- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 Thierry.Onkelinx op inbo.be inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org] Namens Jo?o Fadista Verzonden: dinsdag 8 april 2008 15:18 Aan: r-help op r-project.org Onderwerp: [R] permutation test assumption? Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin?t find any assumption that refers to this subject for permutation tests. Best regards Jo?o Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: Joao.Fadista op agrsci.dk <mailto:Joao.Fadista op agrsci.dk> Web: agrsci.org <agrsci.org> ________________________________ DJF now offers new degree programmes <agrsci.org/content/view/full/34133> . News and news media <agrsci.org/navigation/nyheder_og_presse> . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]]
Dear Thierry, Thanks for the reply. But as you may read in the paper bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 when the sample sizes are not the same there may be an increase in the Type I error rate. Comments will be appreciated. Best regards, Jo?o Fadista ________________________________ De: ONKELINX, Thierry [mailto:Thierry.ONKELINX at inbo.be] Enviada: ter 08-04-2008 15:27 Para: Jo?o Fadista; r-help at r-project.org Assunto: RE: [R] permutation test assumption? Dear Jo?o, You can do permutation tests on an unbalanced design. HTH, Thierry ---------------------------------------------------------------------------- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 Thierry.Onkelinx at inbo.be inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Namens Jo?o Fadista Verzonden: dinsdag 8 april 2008 15:18 Aan: r-help at r-project.org Onderwerp: [R] permutation test assumption? Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin?t find any assumption that refers to this subject for permutation tests. Best regards Jo?o Fadista Ph.d. student UNIVERSITY OF AARHUS Faculty of Agricultural Sciences Dept. of Genetics and Biotechnology Blichers All? 20, P.O. BOX 50 DK-8830 Tjele Phone: +45 8999 1900 Direct: +45 8999 1900 E-mail: Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> Web: agrsci.org <agrsci.org> ________________________________ DJF now offers new degree programmes <agrsci.org/content/view/full/34133> . News and news media <agrsci.org/navigation/nyheder_og_presse> . This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. [[alternative HTML version deleted]]
On Wed, 9 Apr 2008, Jo?o Fadista wrote:> Dear Thierry, > > Thanks for the reply. But as you may read in the paper > bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 > when the sample sizes are not the same there may be an increase in the > Type I error rate.No, this is false and not what the reference above says. Please read more carefully.> Comments will be appreciated.The basic assumption for permutation tests is exchangeability of the observations (regardless of sample sizes). The reference above describes a situation when this assumption is violated. Z> Best regards, > Jo?o Fadista > > > ________________________________ > > De: ONKELINX, Thierry [mailto:Thierry.ONKELINX at inbo.be] > Enviada: ter 08-04-2008 15:27 > Para: Jo?o Fadista; r-help at r-project.org > Assunto: RE: [R] permutation test assumption? > > > > Dear Jo?o, > > You can do permutation tests on an unbalanced design. > > HTH, > > Thierry > > > ---------------------------------------------------------------------------- > ir. Thierry Onkelinx > Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest > Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance > Gaverstraat 4 > 9500 Geraardsbergen > Belgium > tel. + 32 54/436 185 > Thierry.Onkelinx at inbo.be > inbo.be > > To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. > ~ Sir Ronald Aylmer Fisher > > The plural of anecdote is not data. > ~ Roger Brinner > > The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > -----Oorspronkelijk bericht----- > Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Namens Jo?o Fadista > Verzonden: dinsdag 8 april 2008 15:18 > Aan: r-help at r-project.org > Onderwerp: [R] permutation test assumption? > > Dear all, > > Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin?t find any assumption that refers to this subject for permutation tests. > > > Best regards > > Jo?o Fadista > Ph.d. student > > > > UNIVERSITY OF AARHUS > Faculty of Agricultural Sciences > Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Phone: +45 8999 1900 > Direct: +45 8999 1900 > E-mail: Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> > Web: agrsci.org <agrsci.org> > ________________________________ > > DJF now offers new degree programmes <agrsci.org/content/view/full/34133> . > > News and news media <agrsci.org/navigation/nyheder_og_presse> . > > This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > >
But in that paper they refer to another (bepress.com/cgi/viewcontent.cgi?article=1053&context=ucbbiostat) where they say that "permutation distribution produces an asymptotically correct null distribution if (i) the sample sizes are equal...". Best regards, Jo?o ________________________________ De: Achim Zeileis [mailto:Achim.Zeileis at wu-wien.ac.at] Enviada: qua 09-04-2008 0:26 Para: Jo?o Fadista Cc: ONKELINX, Thierry; r-help at r-project.org Assunto: Re: [R] permutation test assumption? On Wed, 9 Apr 2008, Jo?o Fadista wrote:> Dear Thierry, > > Thanks for the reply. But as you may read in the paper > bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2244 > when the sample sizes are not the same there may be an increase in the > Type I error rate.No, this is false and not what the reference above says. Please read more carefully.> Comments will be appreciated.The basic assumption for permutation tests is exchangeability of the observations (regardless of sample sizes). The reference above describes a situation when this assumption is violated. Z> Best regards, > Jo?o Fadista > > > ________________________________ > > De: ONKELINX, Thierry [mailto:Thierry.ONKELINX at inbo.be] > Enviada: ter 08-04-2008 15:27 > Para: Jo?o Fadista; r-help at r-project.org > Assunto: RE: [R] permutation test assumption? > > > > Dear Jo?o, > > You can do permutation tests on an unbalanced design. > > HTH, > > Thierry > > > ---------------------------------------------------------------------------- > ir. Thierry Onkelinx > Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest > Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance > Gaverstraat 4 > 9500 Geraardsbergen > Belgium > tel. + 32 54/436 185 > Thierry.Onkelinx at inbo.be > inbo.be > > To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. > ~ Sir Ronald Aylmer Fisher > > The plural of anecdote is not data. > ~ Roger Brinner > > The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > -----Oorspronkelijk bericht----- > Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Namens Jo?o Fadista > Verzonden: dinsdag 8 april 2008 15:18 > Aan: r-help at r-project.org > Onderwerp: [R] permutation test assumption? > > Dear all, > > Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin?t find any assumption that refers to this subject for permutation tests. > > > Best regards > > Jo?o Fadista > Ph.d. student > > > > UNIVERSITY OF AARHUS > Faculty of Agricultural Sciences > Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Phone: +45 8999 1900 > Direct: +45 8999 1900 > E-mail: Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> > Web: agrsci.org <agrsci.org> > ________________________________ > > DJF now offers new degree programmes <agrsci.org/content/view/full/34133> . > > News and news media <agrsci.org/navigation/nyheder_og_presse> . > > This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > >