Dear Lukas, Thanks for your response which was very helpful. Jonathan On Thu, Aug 15, 2013 at 06:53:42PM -0700, Lukas Chavez wrote: > Hi Jonathan, > > CpG density normalization of MeDIP-seq data is still possible using MEDIPS > v >= 1.10.0: by setting the parameter MeDIP of the MEDIPS.meth() function > to MeDIP=TRUE, the resulting table will contain an additional column for > CpG density normalized rms values per sample. > > In principle, the concept of CpG density normalization remains the same and > the dependency between CpG density and read coverage can still be examined > by plotting the calibration plot. However, there are several conceptional > modifications in the new version that will result in differences when > comparing results of the original and of the updated version. For example, > read coverage and CpG density normalization is performed directly on the > targeted window size (e.g. genome wide 300bp windows) and not at smaller > (50bp) bins any more. Consequently, calculation of ams values became > obsolete. In section 7.7 of the manual, I briefly describe concerns I have > today with deducing percentage methylation from CpG density normalized rms/ > ams values. > > In summary, i) I recommend to use rms values for comparisons to bisulfite > data, ii) I consider it to be problematic to deduce percentage methylation > from the rms values without additional knowledge (see section 7.7 of the > manual), and iii) I would like to emphasize that the main focus of the new > MEDIPS package is clearly on the identification of genome wide differential > methylation (or differential coverage in general) between groups of samples. > > All the best, > Lukas > > > > On Thu, Aug 15, 2013 at 6:02 PM, Jonathan Ellis > <jonathan.ellis at="" qimr.edu.au="">wrote: > > > Dear Lukas and Bioconductors, > > > > I have been asked to look at a MeDIP-Seq dataset that has been processed > > with a previous version of the MEDIPS package (version 1.2.0) and I've > > noticed there have been some changes with regards to the current version > > I have installed (version 1.10.0). In particular, it appears as though > > the whole concept of AMS (absolute methylation score) has been dropped > > from the most recent version. > > > > The previous analysis of the data I'm currently looking at used AMS > > values, and I hoping someone can tell me why it's no longer used (e.g., > > is it no longer considered a useful metric, or is there something else > > that better describes the methylation?). > > > > The 1.2.0 version documentation contains the following (on page 27): > > > > "We have shown that such summarized methylation values for ROIs, > > especially the ams values, are most suitable for comparing MeDIP data to > > e.g., bisulhpite sequencing or whole genome shotgun bisulphite > > sequencing data" > > > > If this is correct, what is the best metric to use for such comparisons > > now ams values are no longer being produced? > > > > Thanks, > > Jonathan > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > >