how to check significant differential methylation, hypermethylated or hypomethylated betweem case and control groups?
Hi,
I have DNA methylation samples from two groups of patients (case, control) where I would like to know if the differential methylation is significant and it is hypermethylated or hypomethylated.
Check differential methylation is significant:
pvalue < 0.05 and absolute Delta M?
Is it correct to calculate delta M like this: Delta M = mean(case_levels) - mean(normal_levels)
What it Delta M threshold? Is |delta_m| > 2?
How to know the region is hypermethylated or hypomethylated?
hypermethylated if delta_m > 2 hypomethylated? if delta_m < -2
Thanks a lot!
• 1,105 views
•
link
written
by
carlos_marchi
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Differential methylation in gene
written by Mamatha Y S •
-
RnBeads mean difference vs M-values
written by a.basitkhan1990 •
-
log2fC from limma on methylation analysis
written by adeizadavid •
-
differential expressed proteins cutoff threshold
written by dew •
-
can we perform Enrichment analysis for Insignificant genes (padj <0.05)
written by majeedmj.ict •
-
R or python packages for differential methylation levels analysis: case x control
written by carlos_marchi
-
Volcano plot with highlighted significantly up/down regulated genes with specific normalised reads …
written by camillab. •
-
How to calculate differential methylation from nanopore reads?
written by O.rka
-
Correlation between gene expression and methylation
written by tujuchuanli
-
Methylation analysis with MEDIPS
written by ilyco •
have you googled for "differential methylation test" or "differential methylation software"? Please don't do this manually or by writing any test code yourself. This is something for which robust software exists. (e.g. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1664-9)