Hi dmpFinder uses beta-values for fetching the differentially methylated positions. 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)? 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 [[alternative HTML version deleted]]

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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]