Hello,
I checked the expression of several genes from different strains and I obtained the values of the relative normalized expression of each gene from each strain compared to the relative gene in my reference strain. So I have the relative expression of gene X in strain 1, 2 or 3, compared to gene X in strain 0 and I want to see if these values are significant (I have 3 biological replicates each). What is more appropriate in this case?
If you are not interested in which strains differ, ANOVA is ok.
If you want to compare strains pair-wise, you have to do t-tests. However, you should try to use a pooled variance estimate (because it's more robust) and it might be good to control the family-wise error-rate across the possible tests. This is achieved e.g. by Tukey's HSD test.
If your goal is to see if different genes react differently in the different strains, then you should fit a two-factorial model (gene is one factor, strain is the other factor).
ANOVA would work best -
http://www.sthda.com/english/wiki/one-way-anova-test-in-r
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