[BioC] poe.mcmc - phenotypic label - coding

[mjonczyk]

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
>>
>>
>>
>> --
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