Hello everyone,
Please I need your help as I find myself in a bit of a conundrum. I'm trying to perform a multiple hypothesis testing with the Bonferroni method and while it seems clear in theory, I have no idea how to proceed with R studio.
So for context: I'm working on a dataset with 3 columns (gene name, gene expression, growth rate). The goal here is to pick out 10 gene that are involved in the growth rate. As I have 5537 different genes, I am aware that I should do a Multiple Hypothesis Test and then use the bonferroni methode and that's where things get tricky.
I have no idea on how to calculate 5537 hypotheses and somehow strore their p-value not to mention applying Bonferroni method to the p-values
I would greatly appreciate your help,
Thank you
could you define the nature of the gene expression values (raw reads, TPM, fpkm, z-score, etc..). Also what did you already try ?
No idea what you are trying in details but any of the standard correction methods can be applied with
p.adjust()on a vector of p-values.