In my current research Project I am comparing gene abundances thorugh time from 6 different sources. I want to know if there is a significant difference between Samples coming from the same source through time, and if there is a significant difference between sources. After executing the two-way ANOVA, I've found that the source of the sample is significantly different. (1 Factor is significant, the other is not.)
I have done the bonferroni Correction for a One way ANOVA before, and then did multple t-test s with the altered alpha value to determine difference. Can I do the same in this situation?
Sure, it is just an inequality so the more dependent the p-value are the more conservative, but it is an accepted inequality for any set of p values. Worth noting that in most cases Holm's modified approach is preferred.
Have you considered using the false discovery rate (FDR) approach instead? You can read about it at the bottom of this page:
https://www.biostathandbook.com/multiplecomparisons.html
HTH.
If you wish to be really modern look at these the computer codes are described in the introduction. Best wishes David Booth
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