On Wed, Mar 20, 2013 at 8:20 PM, Subhashree <subhi.2k7@gmail.com> wrote:

> dmpFinder uses beta-values for fetching the differentially methylated
> positions.


No it doesn't.  Look at the function:

    if (is(dat, "MethylSet")) {
        M <- getM(dat)
    } else {
        stopifnot(is.numeric(dat))
        M <- dat
        if (is.vector(M)) M <- matrix(M, nrow=1)
    }

I would like to know if using the SWAN normalized M-values can be
> used for the same? And, if that's a suitable approach, how to go about it
> (convert the M-vales to beta-values and then perform dmpFinder on these
> values; does it require logit transform as well)?
>

If you want to run dmpFinder on SWAN-normalized M-values (which may or may
not be the best idea, depending on your experimental objective), feed it a
MethylSet that has been through preprocessSWAN(rgSet).  You should be able
to do this from raw data to DMPs in just a few lines of code.  Read the
help pages for preprocessSWAN() and read.450k.exp().

## ...modified from the vignette...
RGset <- read.450k.exp(base = yourBaseDir, targets = yourTargets)
Mset.Ilmn <- preprocessIllumina(RGset)
Mset.swan <- preprocessSWAN(RGset, Mset.Ilmn)

## run dmpFinder on the resulting SWAN-normalized data
dmp <- dmpFinder(Mset.swan, pheno=Mset.swan$group, type="categorical")



>
>
>
> I have actually run dmpFinder on the M-values, post SWAN normalization
> (without any conversion to beta values or without any transformation), and
> like the previous post, I would like to know the methylation status of the
> differential positions, but am unsure about the approach to be taken for
> the
> same. And all the same, I am unable to understand whether the value of
> intercept should be of any concern to me..
>
>
>
> Kindly help!!
>
>
>
> Thanks in advance
>
>
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>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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