Hi,
I am new to bioinformatics, coding, R and my stats knowledge is far from ideal. I need to compare three groups and it seems I can do that using limma since lmFit + eBayes calculates F values which are also used by ANOVA, right? To my understating, I would have to make sure my design matrix is appropriate and use contrast.fit() to make the group comparisons; however, I have no idea where to start. I searched for ANOVA in limma's manual but very little explanation was provided (or I was not able to find it). I would appreciate it if someone could help me design the matrix and how to perform the ANOVA. If possible, I would also appreciate a good resource where I can learn to design theses matrices.
I have 3 groups (G), each with 2 biological replicates (B) and 3 technical replicates (R).
| G1_B1_R1 | G1_B1_R2 | G1_B1_R3 | G1_B2_R1 | G1_B2_R2 | G1_B2_R3 |
| G2_B1_R1 | G2_B1_R2 | G2_B1_R3 | G2_B2_R1 | G2_B2_R2 | G2_B2_R3 |
| G3_B1_R1 | G3_B1_R2 | G3_B1_R3 | G3_B2_R1 | G3_B2_R2 | G3_B2_R3 |
Please, let me know if you need any extra information or if it is too confusing and I will do my best to make it as clear as possible.
Cheers, Luiz