My question is about what is the best option for “matrix design” taking into account that I am Converting to relative quantities with average.

As I said earlier Smile , my experiment is in plants and I am interested in compare the expression of four genes in leaves and root (tissue= first factor), of three varieties of this plant (varieties = second factor). For each tissue in each variety I have three biological replicates (18 samples)

In this way, what is the best matrix (or matrices) among the follow option:

1. One big matrix of 18 x 5 (5 = genes plus housekeeping). In this way, with this Matrix I will do the data pre-processing (Converting to relative quantities with average)

2. Three matrices for each variety. Each matrix is of 6 x 5 (6 = 2 tissues with three biological replications). Independently each matrix is worked in pre-processing.

3. Six matrices for Tissue and for variety. Each matrix is of 3 x 4 (three biological replicates). Independently each matrix is worked in pre-processing.

With this pre-processed data I want to do:

1. Univariable comparisons: a. Leafs to Roots in each variety (pair experiment), b. Leafs among varieties and c. Roots among varieties.

2. Multivariable comparison among the four genes (if is possible).

Thank you very much for you help.

Best Regards!!!

Morgan