[BioC] missing value where TRUE/FALSE needed (metaArray)

[mjonczyk]

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]
> >
> > _______________________________________________
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> >
>
> --
> 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:
------
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[4] https://stat.ethz.ch/mailman/listinfo/bioconductor
[5] http://news.gmane.org/gmane.science.biology.informatics.conductor
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