i had microarray data sample files (.CEL files). i had used limma package & found out topTable of differentially expressed genes in R . But now i have some samples in which more than one factors have been applied i.e. strain, time, treatment etc. So i am not able to construct design matrix. Although in limma user guide has given an example of estrogen datasets but i didn't get it.
please help me if anyone have any idea regarding object of experimental design. How can we add factor with raw data i.e. .CEL files. please give the answer with any example if you can.