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

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