Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
0
0
Entering edit mode
@peterfransquet-15875
Last seen 6.3 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 • 1.4k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
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

Login before adding your answer.

Traffic: 663 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6