Good day, I'm studying the DNA methylation using Champ package in R-studio. I have some questions about LogFC and delta-beta value in the result generated by the champ package. The authors have mentioned that logFC and delta value are having the same value in the documentation.

Blockquote (delta value is same as logFC, we kept is here because very old version ChAMP used).

When I tested with the test data and I got the same logFC and delta value. But when I tested with another set of data, the results are different for the logFC and delta value (different in positive and negative). May I know Is that normal? Another question is, May I know for is that the input data set need to follow the format (maybe certain header pattern) like the one in the test data?

Thank you very much,

Hongbii

I think it's normal if it's just a positive negative difference.

ChAMP function sometimes will "sort" your phenotypes, so if you want to compare "B" to "A", but after the calculation, the result might be from "A" to "B", then if so, the values are negatively calculated. I may try improve this in future version.

But for now, if you get result, you may check the graph or beta value to confirm which one is higher. I normally only use abs(LogFC) or abs(Delta) for filtering. I think there is an average value for each group in the result you may refer to.