Some confusions about DSS

[nedevil]

Hi Wu,
I have some questions when using DSS to analysis differential methylation Sites on my WGBS methylation data:
1. I combined + - strands CG reads counts together to represent the methylation counts on that sites in the assumption that DNMT1 maintaince of the CpG methylation on both strands. (for example, input chr1 10469 5 3 \n chr 10470 7 4 is combined into chr1 10469 12 7). Is it fine to combine it when the warning "CG positions in chromosome chr1 is not ordered. Reorder CG sites." occurs?
2. In my understading when reading the paper, it consider all the samples in one group to estimate the β distribution of the methylation on one sites. So Is it require the high consistence in a group? How about the performance when control group(healthy) is consistent while the other group(tumor) is really chaos among the samples?
Thanks a lot!

[haowulab]

1. The warning message appears when the input data are not sorted by CG site locations. It won't affect your data analysis. DSS will sort them. This has nothing to do with combining +/- strands
2. No it doesn't require "high consistence". When consistence is low, the within group variance will be higher.

[nedevil]

1. The warning message appears when the input data are not sorted by CG site locations. It won't affect your data analysis. DSS will sort them. This has nothing to do with combining +/- strands
2. No it doesn't require "high consistence". When consistence is low, the within group variance will be higher.

It's very useful. Thank you very much !