I hope someone can help me out in defining the right design formulas and contrasts to use with DESeq2 for a (subjectively) rather complex experimental design.
The two infection types infA and infB were considered to be equivalent by the experimental scientists.
The experimental design was as follows:
And the questions i would like to pose with DESeq2 are:
- how do the KO cells differ in their response to any treatment compared to WT cells.
- how do the KO cells differ in their response to treatment A (infA) compared to WT cells.
- how do the KO cells differ in their response to treatment B (infB) compared to WT cells.
any suggestions on design formulas and contrasts to use are very much appreciated.
i am really sorry for not providing a suggestion myself, but i am afraid that might get embarrassing
THANKS
The two infection types infA and infB were considered to be equivalent by the experimental scientists.
The experimental design was as follows:
Code:
genotype sex inf_type inf m_KO_iA KO m infA inf m_KO_1 KO m NOinf NOinf m_KO_iB KO m infB inf m_KO_2 KO m NOinf NOinf m_WT_iA WT m infA inf m_WT_1 WT m NOinf NOinf m_WT_iB WT m infB inf m_WT_2 WT m NOinf NOinf f_KO_A KO f infA inf f_KO_1 KO f NOinf NOinf f_KO_iB KO f infB inf f_KO_2 KO f NOinf NOinf f_WT_iA WT f infA inf f_WT_1 WT f NOinf NOinf f_WT_iA WT f infA inf f_WT_2 WT f NOinf NOinf
- how do the KO cells differ in their response to any treatment compared to WT cells.
- how do the KO cells differ in their response to treatment A (infA) compared to WT cells.
- how do the KO cells differ in their response to treatment B (infB) compared to WT cells.
any suggestions on design formulas and contrasts to use are very much appreciated.
i am really sorry for not providing a suggestion myself, but i am afraid that might get embarrassing
THANKS
Comment