Question

Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array

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peter.fransquet • 0

@peterfransquet-15875

Last seen 5.7 years ago

Hi All,

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,

https://imgur.com/GOrqVfM

The sample passed detectionP no problems, do you think its distribution on the graph is means to remove the sample?

Kind Regards,
Pete

minfi normalization outliers dna methylation densityplot • 1.1k views

ADD COMMENT • link 5.7 years ago peter.fransquet • 0

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Further, if anyone can tell me how to derive my own answer i would greatly appreciate the opportunity to learn how!

ADD REPLY • link 5.7 years ago peter.fransquet • 0

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Its a tough one. From the density plot it is a bit of an outlier which is never a good sign. On the other hand, the density per se does not look horrible. I would say it requires more information On Wed, Jul 25, 2018 at 10:54 PM peter.fransquet [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User peter.fransquet <https: support.bioconductor.org="" u="" 15875=""/> wrote Comment: > Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array > <https: support.bioconductor.org="" p="" 111398="" #111399="">: > > Further, if anyone can tell me how to derive my own answer i would greatly > appreciate the opportunity to learn how! > ------------------------------ > > Post tags: minfi, normalization, outliers, dna methylation, epic > microarray > > You may reply via email or visit > C: Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array >

ADD REPLY • link 5.7 years ago Kasper Daniel Hansen ★ 6.5k