using timecourse package with non-replicated time course
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@johannes-meisig-4755
Last seen 9.6 years ago
Hi, I have a developmental microarray time course with 18 time points under one biological condition but no replicates. I would like to rank genes in order of non-constancy. The timecourse package seems well suited to this analysis. However, in the documentation it says nothing about the no replicate case. In Tai and Speed(1), it seems that the method still works in this special case. Does anyone know if the timecourse package can be used in this case? Thanks a lot, Johannes (1) Tai and Speed, A Multivariate Empirical Bayes Statistic for Replicated Microarray Time Course Data, The Annals of Statistics, 34, 2006
Microarray TimeCourse timecourse Microarray TimeCourse timecourse • 1.5k views
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@johannes-meisig-4755
Last seen 9.6 years ago
Hi, I have a developmental microarray time course with 18 time points under one biological condition but no replicates. I would like to rank genes in order of non-constancy. The timecourse package seems well suited to this analysis. However, in the documentation it says nothing about the no replicate case. In Tai and Speed(1), it seems that the method still works in this special case. Does anyone know if the timecourse package can be used in this case? Thanks a lot, Johannes (1) Tai and Speed, A Multivariate Empirical Bayes Statistic for Replicated Microarray Time Course Data, The Annals of Statistics, 34, 2006
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Yu Chuan Tai ▴ 440
@yu-chuan-tai-1534
Last seen 9.6 years ago
Hi Johannes, Thanks for your interest in timecourse. However, the current timecourse only works for developmental longitudinal time course data *with* replicates. Therefore, it doesn't work for your data. Hope this helps. Best, Yu Chuan On Thu, 14 Jul 2011, Johannes Meisig wrote: > Hi, > > I have a developmental microarray time course with 18 time points under > one biological condition but no replicates. I would like to rank genes > in order of non-constancy. > > The timecourse package seems well suited to this analysis. However, in > the documentation it says nothing about the no replicate case. In Tai > and Speed(1), it seems that the method still works in this special case. > Does anyone know if the timecourse package can be used in this case? > > Thanks a lot, > Johannes > > (1) > Tai and Speed, A Multivariate Empirical Bayes Statistic for Replicated > Microarray Time Course Data, The Annals of Statistics, 34, 2006 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Try mfuzz for time course with no replicates Cheers Paul -----Original Message----- From: Yu Chuan Tai <yuchuan@stat.berkeley.edu> To: Johannes Meisig <j.meisig@biologie.hu-berlin.de> Cc: bioconductor@r-project.org <bioconductor@r-project.org> Subject: Re: [BioC] using timecourse package with non-replicated time course Date: Fri, 15 Jul 2011 12:02:07 +1000 Hi Johannes, Thanks for your interest in timecourse. However, the current timecourse only works for developmental longitudinal time course data *with* replicates. Therefore, it doesn't work for your data. Hope this helps. Best, Yu Chuan On Thu, 14 Jul 2011, Johannes Meisig wrote: > Hi, > > I have a developmental microarray time course with 18 time points under > one biological condition but no replicates. I would like to rank genes > in order of non-constancy. > > The timecourse package seems well suited to this analysis. However, in > the documentation it says nothing about the no replicate case. In Tai > and Speed(1), it seems that the method still works in this special case. > Does anyone know if the timecourse package can be used in this case? > > Thanks a lot, > Johannes > > (1) > Tai and Speed, A Multivariate Empirical Bayes Statistic for Replicated > Microarray Time Course Data, The Annals of Statistics, 34, 2006 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Thanks a lot for the quick answers! Best, Johannes Paul Leo wrote: > Try mfuzz for time course with no replicates > > Cheers > Paul > > > > > -----Original Message----- > *From*: Yu Chuan Tai <yuchuan at="" stat.berkeley.edu=""> <mailto:yu%20chuan%20tai%20%3cyuchuan at="" stat.berkeley.edu%3e="">> > *To*: Johannes Meisig <j.meisig at="" biologie.hu-berlin.de=""> <mailto:johannes%20meisig%20%3cj.meisig at="" biologie.hu-="" berlin.de%3e="">> > *Cc*: bioconductor at r-project.org <bioconductor at="" r-project.org=""> <mailto:%22bioconductor at="" r-project.org%22%20%3cbioconductor="" at="" r-project.org%3e="">> > *Subject*: Re: [BioC] using timecourse package with non-replicated time > course > *Date*: Fri, 15 Jul 2011 12:02:07 +1000 > > Hi Johannes, > > Thanks for your interest in timecourse. However, the current timecourse > only works for developmental longitudinal time course data *with* > replicates. Therefore, it doesn't work for your data. > > Hope this helps. > > Best, > Yu Chuan > > On Thu, 14 Jul 2011, Johannes Meisig wrote: > >> Hi, >> >> I have a developmental microarray time course with 18 time points under >> one biological condition but no replicates. I would like to rank genes >> in order of non-constancy. >> >> The timecourse package seems well suited to this analysis. However, in >> the documentation it says nothing about the no replicate case. In Tai >> and Speed(1), it seems that the method still works in this special case. >> Does anyone know if the timecourse package can be used in this case? >> >> Thanks a lot, >> Johannes >> >> (1) >> Tai and Speed, A Multivariate Empirical Bayes Statistic for Replicated >> Microarray Time Course Data, The Annals of Statistics, 34, 2006 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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