Number of Comparisons in Bonferroni Correction

Question

[khatami.mahshid]

Hi,

I have a list of variants and each of them has a different number of donors in 3 groups. for example:

var1:
group1:10-
group2:20-
group3:25

var2:
group1:20-
group2:15-
group3:20

var3:
...

I have a p-value of each variant, but I don't know what is the number of test for converting p-value to adjusted p-value of Bonferroni.

can anyone help me?

thank you

[Benn]

The number of variants, is the number of tests you have used.

[khatami.mahshid]

but each variant is independent and I do not compare variants with each other.

[shawn.w.foley]

Bonferroni (and all multiple testing corrections) corrects for each test that you performed. If you have 1000 variants, and you have 1000 p-values, then you've performed 1000 tests. Even if they're independent, with a p-value of 0.05 performing 1000 tests would still results in 50 "significant" results just by chance.

You might want to consider performing a Benjamini-Hochberg (or FDR) correction instead of a Bonferroni as it's less conservative.

[Benn]

Okay it sounds like you do not completely understand the 'why' you should correct for multiple testing (no offense). Best is to read more about it, for example here some background about the test.

If you have many variants, you would be better off using a less conservative method, like Benjamini-Hochberg.