I am trying to use HTqPCR to assemble data exported from a Roche480 96wp Lightcycler which may be in an atypical format, with 24 cDNA samples in adjacent technical duplicate assayed with primers against target gene 1 in file lines 3-50 and the same 24 samples assayed with primers against target gene 2 in lines 51-98. 

My question is whether or not there is a batch correction function based on means or medians which I can apply prior to the various normalization functions in the package, and what that would be called. For instance if one batch of 24 samples routinely has high Ct values compared to other batches I would like to adjust the Cp values by a factor related to the original and target median Cp values.