Dear ALL,

i have preprossed and normalized 10 CEL files, which include one control sample group and 4 biological substances, each constisted of two biological replicates. My phenoData object is the following:

Data(normalized2)
                           condition               replicate
dataset_603.dat       Control                  1
dataset_604.dat       Control                  2
dataset_605.dat       Substance1           1
dataset_606.dat       Substance1           2
dataset_607.dat       Substance2           1
dataset_608.dat       Substance2           2
dataset_609.dat       Substance3           1
dataset_610.dat       Substance3           2
dataset_611.dat       Substance4           1
dataset_612.dat       Substance4           2

Due to the obvious limitation of replicates, im considering of performing rank products for the comparizon of each substance to the control(i.e. 3 different treatments vs control) to see if i could find any DE genes in every treatment. Moreover, as the argument cl of the function RP needs  a vector for the two classes of comparison(0 for control and 1 for case group), i would like to ask if it is possible to perform a paired analysis for each treatment, in a way that each substance matches to its biological replicate(i.e Substance1 vs Control 1 and Substance2 vs Control2 for the Substance 1 vs Control). Any possible ideas or help ??

Thank you in advance !!!