I would like to know whether bsseq package works with technical replicates (i.e. two whole-genome bisulfite sequencing of the same DNA sample). How bsseq deal with replicate information? The code below exemplifies what I have done.
> pData(bismarkBSseq) DataFrame with 8 rows and 2 columns Type Rep <factor> <character> C1_R1 Control replicate1 C2_R1 Control replicate1 T1_R1 Treatment replicate1 T2_R1 Treatment replicate1 C1_R2 Control replicate2 C2_R2 Control replicate2 T1_R2 Treatment replicate2 T2_R2 Treatment replicate2