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

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/

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 >>