What is an acceptable false discovery rate?

When you report your results, you should make FDR to 0.1 or 0.05 unless you have a good reason not to. Your report will be consistent to the literature because other people also use 0.1 or 0.05. If you set your FDR to something like 0.0456, your paper might be rejected for inconsistency.

How can false discovery rates be avoided?

False discovery rate control

1. Modern methods do not always control the FDR.
2. lfdr and fdrreg-t do not control FDR with few tests.
3. lfdr and ashq do not control FDR for extreme proportions of non-null tests.
4. Modern methods are modestly more powerful.
5. Power of modern methods is sensitive to covariate informativeness.

Is false discovery rate the same as P value?

The false discovery rate is the complement of the positive predictive value (PPV) which is the probability that, when you get a ‘significant’ result there is actually a real effect. So, for example, if the false discovery rate is 70\%, the PPV is 30\%.

What is false discovery rate in mass spectrometry?

False discovery rate (FDR) is a measure of the incorrect PSMs among all accepted PSMs [2, 3, 4]. Proposed by Benjamini and Hochberg [5] as an alternate to the Bonferroni correction, it is defined as the rate of false positives in accepted hits.

Why is false discovery rate important?

False Discovery Rate estimates are an effective solution to multiple testing problem. There is no downside to using them; they can be very simple to calculate (we show you how to do that here[3]); and the information FDR provides is dramatically more informative than a P-value.

What is false discovery rate in statistics?

The false discovery rate (FDR) is a statistical approach used in multiple hypothesis testing to correct for multiple comparisons. The FDR is defined as the expected proportion of false discoveries, i.e., incorrectly rejected null hypothesis, among all discoveries (Benjamini and Hochberg 1995).

What is a false discovery rate in data mining?

How do you calculate false positive rate?

The false positive rate is calculated as FP/FP+TN, where FP is the number of false positives and TN is the number of true negatives (FP+TN being the total number of negatives). It’s the probability that a false alarm will be raised: that a positive result will be given when the true value is negative.

What is FDR proteomics?

False discovery rate (FDR) is the metric for global confidence assessment of a large-scale proteomics dataset. Keywords: False discovery rate; Peptide spectrum matches; Posterior error probability; Shotgun proteomics; Statistical validation; Target-decoy.

What is peptide spectrum match?

A peptide-spectrum match (PSM) scoring function assigns a numerical value to a peptide-spectrum pair (P,S) expressing the likelihood that the fragmentation of a peptide with sequence P is recorded in the experimental mass spectrum S.

Is FDR better than p-value?

So, FDR offers more confidence than just p-value. Usually, results below 0.05 are considered real. However, this statistic is just telling you if the differences observed are due to chance or not, i.e. if they are real and can be trusted.