about read normalization in methylaction

[diannedai]

Hi, Jeffrey:
The normalized reads in identified differentially methylated region (DMR) are generated in the output. How are reads in DMR normalized? How is the read normalization in the DMR different from the read normalization in the pre-processing?

Thank you very much
Jun Dai
Des Moines University

[jeffbhasin]

Hello Jun,
The normalization in MethylAction is done using the methods of DESeq, so you can also find some more information in their documentation. Thus, within each fixed-width bin, the DESeq scaling methods are used, and accounting for library size is handled at the statistical testing level using the way library size is a term of the GLM in DESeq.

Summarizing the methods from DESeq, for scaled counts, there is a size factor computed which is the ratio between the library size of a sample and the geometric mean of all samples. Counts are scaled by this factor to normalize them for depth.

Jeff