I have a targets file as follows;
file1 GeneInsert 1
file2 GeneInsert 2
file4 EmptyVector 1
file5 EmptyVector 2
file7 no_treatment 1
file8 no_treatment 2
Treat = treatment by tranfsection of an interesting gene, or with an empty vector transfected, and finally cells not treated at all. They are also paired by sibship.
How can I make differential gene expression of GeneInsert vs. no_treatment (but taking into account both the Empty vector and sibship)?
I have read the pertinent sections, 9.4 and 9.5 of the Limma manual, but I am not sure which is, if any, are applicable?
I will appreciate any help, thank you.
Note; for an unpaired analysis I did;
contrast.matrix <- makeContrasts('InsertVscontrol'=GeneInsert-((no_treatment+EmptyVector)/2), levels=design)
Looks to be working as plots of expression values of the signif. diff. expressed genes look as they should (but I would like to incorporate the sibship as well to be precise).