Null|free False Discovery Rate Control Using Decoy Permutations

A new estimation of protein-level false discovery rate - BMC Genomics

We employ the target-decoy technique to determine null distributions. In the permutation step, each sequence in the original protein database is ...

Bias in False Discovery Rate Estimation in Mass-Spectrometry ...

Accurate target-decoy-based false discovery rate (FDR) control of peptide identification from tandem mass-spectrometry data relies on an ...

Weighted False Discovery Rate Control in Large-Scale Multiple ...

Publications that cite this publication · Null-free False Discovery Rate Control Using Decoy Permutations · Influence of multiple hypothesis testing on ...

How do FDR procedures estimate a False Discovery Rate without a ...

I think that's a really good question; too many people use the Benjamini-Hochberg procedure (abbreviated BH; possibly the most popular ...

Multiple Competition-Based FDR Control and Its Application to ...

... false discovery rates by decoy permutations (2018). arXiv preprint ... Null-free False Discovery Rate Control Using Decoy Permutations. Kun He, Meng ...

p-value-free FDR control on high-throughput data from two conditions

In: Nature methods 15.4 (2018), p. 255. [54] Kun He et al. “Null-free False Discovery Rate Control Using Decoy Permutations for Multiple.

A general method for accurate estimation of false discovery rates in ...

... Free full text in Europe PMC · Null-free False Discovery Rate Control Using Decoy Permutations. He K, Li MJ, Fu Y, Gong FZ, Sun XM · Acta Math Appl Sin, 38(2): ...

Supplementary Material to: Multiple competition-based FDR control ...

In the multiple hypotheses testing (MHT) set up we simultaneously test m (null) hy- potheses H1,...,Hm, looking to reject as many as possible subject to ...

Prog-Plot – a visual method to determine functional relationships for ...

Null-free False Discovery Rate Control Using Decoy Permutations. Kun He, Acta Mathematicae Applicatae Sinica (English Series)-1, 2022. A novel method for ...

Multiple Competition-Based FDR Control and Its Application to ...

Using real data to study the peptide detection problem we show that, relative to existing single-decoy methods, our approach can increase the number of ...

A parametric model to estimate the proportion from true null using a ...

2022, Statistical Methods in Medical Research. Null-free False Discovery Rate Control Using Decoy Permutations. 2022, Acta Mathematicae Applicatae Sinica ...

Comments on the analysis of unbalanced microarray data. - Abstract

Using biased P-values to estimate the FDR can produce unacceptable bias in those estimates. Results also show that the approach of pooling permutation null ...

Beyond target-decoy competition: stable validation of peptide and ...

Target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control in bottom-up discovery proteomics. Despite ...

Beyond target-decoy competition: stable validation of peptide ... - HAL

In bottom-up discovery proteomics, target-decoy competition (TDC) is the most pop- ular method for false discovery rate (FDR) control.

CONTROLLING THE FALSE DISCOVERY RATE THROUGH ...

CONTROLLING THE FALSE DISCOVERY RATE THROUGH MULTIPLE COMPETITION ... Null-free False Discovery Rate Control Using Decoy Permutations.

Mascot help: Automatic target-decoy searching and ... - Matrix Science

When the search is complete, the numbers of matches and the false discovery rate (FDR) are reported in the result header. Example of the decoy statistics for an ...

False Discovery Rate (FDR) Tutorial | Protein Identification

Since all the decoy identifications are false, FDR can be estimated by FDR = (# Decoy Hits) / (# target hits). Figure 3: With a properly constructed decoy, the ...

ProteomeXchange Dataset PXD020322

Description, We introduce a new decoy-free framework for false discovery rate (FDR) estimation that generalizes present decoy-free approaches (DFAs) while ...