Multiple T-test

[niki...@gmail.com]

Hi there,

Graphpad offers multiple options to do multiple t-test corrections with the false discovery rate approach:

1. Two-stage step-up method of Benjamini, Krieger and Yekutieli

2. Original FDR of Benjamini and Hochberg

3. Corrected method of Benjamini and Yekutieli

Depending on which one I use, I have different significant proteins and with the first one I get more significant proteins that with the 2nd one (original FDR). Graphpad 7 has as default the two-stage step-up method of Benjamini, Krieger and Yekutieli. I am wondering whether to use this one  or to stick to the conservative originical FDR of Benjamini and Hochberg.

Thank you for your help.

Nikiana

[Veit Schwämmle]

Dear Nikiana,

The most accepted and most commonly used methods are Benjamini Hochberg and the false discovery rates (q-values) by Storey (http://www.pnas.org/content/100/16/9440.full). The latter uses information from the actual distribution of p-values (as the Benjamini, Krieger and Yekutieli method) and therefore requires a certain amount of p-values (at least hundreds) distributed over the entire range (0,1).

It is well possible that you get more significant features this way as this method is less conservative. I suggest to compare the output of method 1 to the one from Storey. The output should be similar.

Best regards

Veit

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[niki...@gmail.com]

Dear Veit,

Thank you very much for your reply.

Best,

Nikiana

On Monday, 23 October 2017 08:34:17 UTC+1, Veit Schwämmle wrote:

Dear Nikiana,

The most accepted and most commonly used methods are Benjamini Hochberg and the false discovery rates (q-values) by Storey (http://www.pnas.org/content/100/16/9440.full). The latter uses information from the actual distribution of p-values (as the Benjamini, Krieger and Yekutieli method) and therefore requires a certain amount of p-values (at least hundreds) distributed over the entire range (0,1).

It is well possible that you get more significant features this way as this method is less conservative. I suggest to compare the output of method 1 to the one from Storey. The output should be similar.

Best regards

Veit

2017-10-19 15:27 GMT+02:00 <niki...@gmail.com>:

Hi there,

Graphpad offers multiple options to do multiple t-test corrections with the false discovery rate approach:

1. Two-stage step-up method of Benjamini, Krieger and Yekutieli

2. Original FDR of Benjamini and Hochberg

3. Corrected method of Benjamini and Yekutieli

Depending on which one I use, I have different significant proteins and with the first one I get more significant proteins that with the 2nd one (original FDR). Graphpad 7 has as default the two-stage step-up method of Benjamini, Krieger and Yekutieli. I am wondering whether to use this one  or to stick to the conservative originical FDR of Benjamini and Hochberg.

Thank you for your help.

Nikiana

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To view this discussion on the web visit https://groups.google.com/d/msgid/proteomicsqa/5873d2a6-88d6-4014-b145-423209307107%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.