poe.mcmc - phenotypic label - coding
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boczniak767 ▴ 740
@maciej-jonczyk-3945
Last seen 4 weeks ago
Poland
Dear List, I'd like to make sure I understand coding of phenotypic label in poe.mcmc function of metaArray correctly. Vector of my arrays' treatments could be presented as: (ctrl, ctrl, ctrl, trt1, trt1, trt1) so as NN value I used vector (1, 1, 1, 0, 0, 0). Documentation for either poe.mcmc, poe.em and fit.em say that "1" means that e=0 (baseline expression), and "0" is for other conditions. Although this three documentation files suggests the same coding, fit.em states that: " cl: A vector of 0s and 1s. Use 1 for normal phenotype and 0 for non-normal phenotype. Note that *this is the opposite of POE MCMC.* If all samples are of unknown phenotype or of the same one, give vector of zeros. When class information is provided, conditional estimation of the mixture is applied. " So is it simply an error in text or should I code my variants differently? Best Wishes! -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
metaArray metaArray • 1.2k views
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@debashis-ghosh-3081
Last seen 10.2 years ago
Dear Dr. Jonczyk, It's an error in the text. Hyungwon should be revising the vignette in future versions of metaArray. Debashis On Tue, Oct 4, 2011 at 8:09 AM, mjonczyk <mjonczyk at="" biol.uw.edu.pl=""> wrote: > Dear List, > > I'd like to make sure I understand coding of phenotypic label in > poe.mcmc function of metaArray correctly. > > Vector of my arrays' treatments could be presented as: > > (ctrl, ctrl, ctrl, trt1, trt1, trt1) so as NN value I used vector (1, > 1, 1, 0, 0, 0). > > Documentation for either poe.mcmc, poe.em and fit.em say that "1" means > that e=0 (baseline expression), > and "0" is for other conditions. > > Although this three documentation files suggests the same coding, > fit.em states that: > " > cl: A vector of 0s and 1s. Use 1 for normal phenotype and 0 for > ? ? ? ? ? non-normal phenotype. Note that > *this is the opposite of POE MCMC.* > If all samples are of unknown phenotype or of the same > ? ? ? ? ? one, give vector of zeros. When class information is > ? ? ? ? ? provided, conditional estimation of the mixture is applied. > " > So is it simply an error in text or should I code my variants > differently? > > Best Wishes! > > -- > Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Institute of Plant Experimental Biology > Faculty of Biology, University of Warsaw > 02-096 Warszawa, Miecznikowa 1 > Poland > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > _______________________________________________ > 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 > -- Debashis Ghosh Departments of Statistics and Public Health Sciences Penn State University University Park, PA 16802 works.bepress.com/debashis_ghosh/
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boczniak767 ▴ 740
@maciej-jonczyk-3945
Last seen 4 weeks ago
Poland
Dear Dr. Ghosh, thank you for the clarification. Best Wishes, Maciej --- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 Poland On Wed, 5 Oct 2011 22:22:08 -0400, Debashis Ghosh wrote: > Dear Dr. Jonczyk, > > It's an error in the text. Hyungwon should be revising the vignette > in future versions of metaArray. > > Debashis > > On Tue, Oct 4, 2011 at 8:09 AM, mjonczyk <mjonczyk at="" biol.uw.edu.pl=""> > wrote: >> Dear List, >> >> I'd like to make sure I understand coding of phenotypic label in >> poe.mcmc function of metaArray correctly. >> >> Vector of my arrays' treatments could be presented as: >> >> (ctrl, ctrl, ctrl, trt1, trt1, trt1) so as NN value I used vector >> (1, >> 1, 1, 0, 0, 0). >> >> Documentation for either poe.mcmc, poe.em and fit.em say that "1" >> means >> that e=0 (baseline expression), >> and "0" is for other conditions. >> >> Although this three documentation files suggests the same coding, >> fit.em states that: >> " >> cl: A vector of 0s and 1s. Use 1 for normal phenotype and 0 for >> ? ? ? ? ? non-normal phenotype. Note that >> *this is the opposite of POE MCMC.* >> If all samples are of unknown phenotype or of the same >> ? ? ? ? ? one, give vector of zeros. When class information is >> ? ? ? ? ? provided, conditional estimation of the mixture is >> applied. >> " >> So is it simply an error in text or should I code my variants >> differently? >> >> Best Wishes! >> >> -- >> Maciej Jonczyk, >> Department of Plant Molecular Ecophysiology >> Institute of Plant Experimental Biology >> Faculty of Biology, University of Warsaw >> 02-096 Warszawa, Miecznikowa 1 >> Poland >> >> >> >> -- >> This email was Anti Virus checked by Astaro Security Gateway. >> http://www.astaro.com >> >> _______________________________________________ >> 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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