[BioC] HTqPCR - limmaCtData using samples with different number of replicates?

[Fletez-Brant, Christopher (NIH/VRC) [C]]

Dear List,

I am using HTqPCR to analyze Fluidigm data (specifically, the 96*96 format).  I have been using specifically limmaCtData to look for differential expression between groups, always having the same number of replicates.  However, I currently have a dataset of several groups with 3 replicates and 1 group with  2 replicates.  As far as I can tell, limmaCtData expects the number of replicates to be the same between groups (i.e. there is only one 'ndups' parameter).  Has anyone else encountered this issue?

Thank you,
Kipper Fletez-Brant