RnBeads and technical replicates in differential analysis
1
0
Entering edit mode
Jon Manning ▴ 40
@jon-manning-3420
Last seen 5.7 years ago
United Kingdom

Hi all,

If I define technical replication using the 'replicate.id.column' option in RnBeads, I get some helpful plots in the exploratory analysis. But I can't tell: are these modelled properly in the differential analysis ('a la' duplicateCorrelation in Limma), or should I deal with them myself? Only a subset of my samples have these replicates- they were mostly run to fill up the chip- so I'm inclined to remove them after the QC/exploratory analyses.

Many thanks,

Jon

rnbeads replicates • 707 views
ADD COMMENT
0
Entering edit mode
rnbeads • 0
@rnbeads-7880
Last seen 10 months ago
Germany

Hi Jon,
If the variables were properly incorporated for the p-value calculation, you should see a table in the differential methylation report generated. In this table you should see the assignment for covariates for each sample in the analysis.

HTH,
Fabian

ADD COMMENT

Login before adding your answer.

Traffic: 322 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