Dear Reema, I'd like to ask you, have you got any help with this issue? I've the same problem. Dear All, Has anybody knows what's wrong here? Thanks for any help, Best Regards, Maciej > Hello All > > I m using metaArray package for my study.But when i m using the > poe.mcmc > function on my data then it gives me the following error.I have > remove all > the NA(missing vaue from the data. Can anybody help me out..Why i am > getting > this error?. > > dat.poe<- poe.mcmc(x1, NN = NULL, id = NULL,M = 2000 > Gibbs Sampler > Burn-in > 100 > 200 > Main iterations > 100 ... > 2000 > Summary by median > Error in while (fit.t[i] - min.fit > inter) { : > missing value where TRUE/FALSE needed -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com

Dear all This message will occur if all the probes have the same value across all samples, I.e. The gene has zero sample variance. You will need to remove these probes from the analysis. Debashis On Sunday, September 25, 2011, mjonczyk <mjonczyk@biol.uw.edu.pl> wrote: > Dear Reema, > > I'd like to ask you, have you got any help with this issue? > I've the same problem. > > Dear All, > > Has anybody knows what's wrong here? > > Thanks for any help, > Best Regards, > Maciej > >> Hello All >> >> I m using metaArray package for my study.But when i m using the poe.mcmc >> function on my data then it gives me the following error.I have remove all >> the NA(missing vaue from the data. Can anybody help me out..Why i am getting >> this error?. > >> > dat.poe<- poe.mcmc(x1, NN = NULL, id = NULL,M = 2000 >> Gibbs Sampler >> Burn-in >> 100 >> 200 >> Main iterations >> 100 > > ... >> >> 2000 >> Summary by median >> Error in while (fit.t[i] - min.fit > inter) { : >> missing value where TRUE/FALSE needed > > > -- > Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Institute of Plant Experimental Biology > Faculty of Biology, University of Warsaw > 02-096 Warszawa, Miecznikowa 1 > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com > > _______________________________________________ > 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 > -- Debashis Ghosh Departments of Statistics and Public Health Sciences Penn State University University Park, PA 16802 works.bepress.com/debashis_ghosh/ [[alternative HTML version deleted]]

Thank You All for fast reply. I've checked row variance and indeed some values must be close to 0. > xv=rowVars(exprs(AFY2me)) > summary(xv) Min. 1st Qu. Median Mean 3rd Qu. Max 0.001699 0.044130 0.105300 0.310600 0.258800 20.960000 Actually this low variance looks strange for me - it is data from experiment with two treatments fungal inoculation and mock inoculation. So I'm suprised - I should check everything once more. I'll also check the code provided by Reema - thank you! --- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 On Mon, 26 Sep 2011 07:18:50 +0800, Hyung Won Choi wrote: > Are there any genes for which variance is zero? > > Hyungwon > > Sent from my Windows Phone > ------------------------- > From: Debashis Ghosh > Sent: Monday, 26 September, 2011 5:51 AM > To: mjonczyk > Cc: reema28sep at gmail.com; bioconductor at r-project.org; Hyung Won Choi > Subject: Re: [BioC] missing value where TRUE/FALSE needed (metaArray) > > Dear all > > This message will occur if all the probes have the same value across > all > samples, I.e. The gene has zero sample variance. You will need to > remove > these probes from the analysis. > > Debashis > > On Sunday, September 25, 2011, mjonczyk wrote: > > Dear Reema, > > > > I'd like to ask you, have you got any help with this issue? > > I've the same problem. > > > > Dear All, > > > > Has anybody knows what's wrong here? > > > > Thanks for any help, > > Best Regards, > > Maciej > > > >> Hello All > >> > >> I m using metaArray package for my study.But when i m using the > poe.mcmc > >> function on my data then it gives me the following error.I have > remove all > >> the NA(missing vaue from the data. Can anybody help me out..Why i > am > getting > >> this error?. > > > >> > dat.poe >> Gibbs Sampler > >> Burn-in > >> 100 > >> 200 > >> Main iterations > >> 100 > > > > ... > >> > >> 2000 > >> Summary by median > >> Error in while (fit.t[i] - min.fit > inter) { : > >> missing value where TRUE/FALSE needed > > > > > > -- > > Maciej Jonczyk, > > Department of Plant Molecular Ecophysiology > > Institute of Plant Experimental Biology > > Faculty of Biology, University of Warsaw > > 02-096 Warszawa, Miecznikowa 1 > > > > > > > > -- > > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com [2] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org [3] > > https://stat.ethz.ch/mailman/listinfo/bioconductor [4] > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [5] > > > > -- > Debashis Ghosh > Departments of Statistics and Public Health Sciences > Penn State University > University Park, PA 16802 > works.bepress.com/debashis_ghosh/ [6] > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com Links: ------ [1] mailto:mjonczyk at biol.uw.edu.pl [2] http://www.astaro.com [3] mailto:Bioconductor at r-project.org [4] https://stat.ethz.ch/mailman/listinfo/bioconductor [5] http://news.gmane.org/gmane.science.biology.informatics.conductor [6] http://works.bepress.com/debashis_ghosh/

Dear Hyungwon, dear All, Data is on log scale. I've checked other two studies which I'm going to merge to metaanalysis and variances' ranges are similar. study 2 Min. 1st Qu. Median Mean 3rd Qu. Max. 0.002281 0.106800 0.309800 0.783000 0.896700 19.610000 study 3 Min. 1st Qu. Median Mean 3rd Qu. Max. 0.000472 0.047810 0.120300 0.344400 0.307800 20.290000 So what is minimal variance which don't cause the error? Thank You, Best Wishes --- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 On Mon, 26 Sep 2011 15:02:23 +0800, Hyungwon Choi wrote: > Also, if your data is not on log scale, please take logs. The model > is under certain uninformative prior and if the data goes out of its > range, the sampler may diverge. > > Please don't hesitate to let me know if it still doesn't work out for > you. > > Hyungwon > > > On 09/26/2011 02:59 PM, mjonczyk wrote: >> Thank You All for fast reply. >> >> I've checked row variance and indeed some values must be close to 0. >>> xv=rowVars(exprs(AFY2me)) >>> summary(xv) >> Min. 1st Qu. Median Mean 3rd Qu. Max >> 0.001699 0.044130 0.105300 0.310600 0.258800 20.960000 >> >> Actually this low variance looks strange for me - it is data from >> experiment with two treatments >> fungal inoculation and mock inoculation. So I'm suprised - I should >> check everything once more. >> >> I'll also check the code provided by Reema - thank you! >>