[BioC] poe.mcmc - phenotypic label - coding

[mjonczyk]

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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