I am new to analyzing DNA methylation data on an array scale. i have worked on a pipeline and done some analysis so i have some basic knowledge but want to start over to make sure my QC and analysis are correct. Thus, i have hit my first bump. After SWAN normalisation, most samples fell into line apart from one that is clearly out on the 'methylated' mode, and a few are a bit hairy in the middle.
please see image here,
The sample passed detectionP no problems, do you think its distribution on the graph is means to remove the sample?