threshold of bonferroni-corrected p-value

Question

[seta]

Hi all,

Could anybody please let me know what is the threshold of Bonferroni-corrected p-value in gene ontology analysis? Thanks in advance

[David W]

It will be whatever threshold (alpha value) you set in calculating the Bonferroni correction (i.e. probably 0.05)

Answer 1

[Parham]

I guess it is very different depending on what you are looking for and how strict you want to conclude your data. I start with 0.001 and if required then I increase it up to 0.05.

[seta]

Thanks. It's for gene ontology analysis, as far as I'm concerned, the threshold of corrected p-value can be considered more than p-value (without correction), but how many?!

[Parham]

If it is corrected yes I have seen people putting the threshold higher up to 0.1. As far as I understood there are no rules on where to cross the line for P value. There is no specific number to tell that every one should go with it. It depends on many things in your data analysis. However, I am not statistician so be careful using my words. Someone correct me if I think the wrong way.

[seta]

Yes, my mean is corrected, I'm not statistician, too. but as far as I know, the lower p-value, more reliable results. I use up to 0.05 p-value without correction, but I have no idea about corrected p-value? please any expert corrected us.