[BioC] MEDIPS no longer producing AMS values

[Jonathan Ellis]

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