[BioC] (minfi) Return value from dmpFinder

[Kasper Daniel Hansen]

These are good comments.  We are in the process of finishing up how we
think we should look for DMRs, but I should fix this anyway.  Might
take a little while, but watch the devel version.

Kasper

On Wed, Nov 7, 2012 at 10:33 AM, Gustavo Fernández Bayón
<gbayon at gmail.com> wrote:
> Hi everybody.
>
> I am currently using minfi for every analysis of Illumina 450k I am working on. But today I have run into what I consider a minor problem, i.e., more a matter of usability IMHO.
>
> Problem is, dmpFinder returns a data.frame with columns for the statistic, the p-value, the q-value and the intercept. And, if I would like to know which CpG's are hyper- or hypo-methylated from that table, I think I couldn't (I am talking about the two-category case here). For that, I would need the value of the second coefficient of the model, the actual slope of the fit.
>
> Besides, I would need to know the order of the levels in the factor used as a phenotype indicator (remember two categories case here), in order to interpret the sign of the slope. And minfi is executing:
>
> pheno <- factor(as.character(pheno))
>
> which makes the previous ordering of the levels go away. I understand the general behavior of dmpFinder, and why its result is the way it is, but shouldn't it be a good idea to act differently in this case? I think that comparison of two groups, and splitting between hyper and hypo-methylated probes is very common.
>
> For now, I think I'll do the t-test, correct with p.adjust, and get the values I need on the fly.
>
> Regards,
> Gustavo
>
>
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