I have successfully applied my proposed method to the following task
1) 10 tissues
2) Unmatched control/treatment (each includes three to five samples. The sample number can differ between the control and treatment within each treatment)
3) There are commonly four distinct (but same) treatments for each tissue
4) mRNA expression was measured by the same array (number of probes ~ 40,000)
Thus, total number of gene expression profiles are 10 (tissue) x 4 (treatments) x 2 (treated/control) x 5 (samples in each category) ~ 400
Then, identification of combinations of genes, tissues and treatments where genes are differently expressed between treatments and controls, is the task. (There are no known pre-knowledges about the combination of genes, treatments and tissues).
I need to have de facto standard method to be compared with mine.
What is the de facto standard method for the following task? - ResearchGate. Available from: https://www.researchgate.net/post/What_is_the_de_facto_standard_method_for_the_following_task [accessed Mar 17, 2016].