Search
Question: p.adjust function fdr and BH
0
gravatar for zhang.jianhai
8 days ago by
zhang.jianhai0 wrote:

Hello,

In the p.adjust R function, there are multiple adjust methods, as shown here: https://www.rdocumentation.org/packages/stats/versions/3.5.0/topics/p.adjust

I read many posts, it seems the "BH" is used for "FDR", but why in the function "BH" and "fdr" are two independent methods?

Another question is  can I understand "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", are used for adjusted p value, and "fdr" is used for false discovery rate? What is the difference between adjusted p value and fdr?

Regards,

Jianhai

ADD COMMENTlink modified 8 days ago by Gordon Smyth34k • written 8 days ago by zhang.jianhai0
3
gravatar for Gordon Smyth
8 days ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

"BH" and "fdr" are the same method. The p.adjust help page (that you've linked to) says that "fdr" is merely an alias for "BH".

"BH", "BY" and "fdr" all produce false discovery rates, again as explained by the help page.

A little history

Originally, p.adjust() didn't have any FDR methods. Then Benjamini and Hochberg's method was added. At that time, Benjamini and Hochberg's method was the only FDR method, so it was just called "fdr". Later on, we added the Benjamini & Yekutieli's method as well, so we needed new names. We called the new method "BY" and renamed the old method to "BH". The old name "fdr" was also kept as well, just for backward compatibility, which is how we ended up with two names for the same thing.

ADD COMMENTlink modified 6 days ago • written 8 days ago by Gordon Smyth34k

Hello Gordon,

Now I understand. Thanks.

Regards

ADD REPLYlink written 8 days ago by zhang.jianhai0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 288 users visited in the last hour