# MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing

@article{Zheng2021MixTwiceLH, title={MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing}, author={Zihao Zheng and Aisha M. Mergaert and Irene M. Ong and Miriam A. Shelef and Michael A. Newton}, journal={Bioinformatics}, year={2021}, volume={37}, pages={2637 - 2643} }

Abstract Summary Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes… Expand

#### References

SHOWING 1-10 OF 39 REFERENCES

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

- Computer Science, Medicine
- Bioinform.
- 2008

'fdrtool' implements a flexible FDR estimation scheme that is unified across different test statistics and variants of FDR, and can be applied to very large scale (in the order of millions of hypotheses) multiple testing problems. Expand

Independent filtering increases detection power for high-throughput experiments

- Mathematics, Medicine
- Proceedings of the National Academy of Sciences
- 2010

In an application to microarray data, it was found that gene-by-gene filtering by overall variance followed by a t-test increased the number of discoveries by 50%, and it was shown that this particular statistic pair induces a lower bound on fold-change among the set of discoveries. Expand

False discovery rates: a new deal

- Medicine, Computer Science
- Biostatistics
- 2017

A new Empirical Bayes approach for large‐scale hypothesis testing, including estimating false discovery rates (FDRs), and effect sizes, and it is argued that the local false sign rate is a superior measure of significance than the local FDR because it is both more generally applicable and can be more robustly estimated. Expand

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

- Biology, Medicine
- Nature Methods
- 2016

Independent hypothesis weighting (IHW) is described, a method that assigns weights using covariates independent of the P-values under the null hypothesis but informative of each test's power or prior probability of thenull hypothesis. Expand

Empirical Bayes Analysis of a Microarray Experiment

- Mathematics
- 2001

Microarrays are a novel technology that facilitates the simultaneous measurement of thousands of gene expression levels. A typical microarray experiment can produce millions of data points, raising… Expand

The positive false discovery rate: a Bayesian interpretation and the q-value

- Mathematics
- 2003

Multiple hypothesis testing is concerned with controlling the rate of false positives when testing several hypotheses simultaneously. One multiple hypothesis testing error measure is the false… Expand

Whole Genome-Derived Tiled Peptide Arrays Detect Prediagnostic Autoantibody Signatures in Non-Small-Cell Lung Cancer.

- Medicine, Biology
- Cancer research
- 2019

Data show that tiled peptide arrays provide a means to delineate epitopes encoded across the genome that trigger an autoantibody response associated with tumor development, and provide a modality for early diagnosis of NSCLC for precision oncology that can be applied to other cancer types. Expand

Hierarchical Mixture Models for Expression Profiles

- Mathematics
- 2006

A class of probability models for inference about alterations in gene expression is reviewed. The class entails discrete mixing over patterns of equivalent and differential expression among different… Expand

Controlling the false discovery rate: a practical and powerful approach to multiple testing

- Mathematics
- 1995

SUMMARY The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to… Expand

Affinity Purification and Comparative Biosensor Analysis of Citrulline-Peptide-Specific Antibodies in Rheumatoid Arthritis

- Chemistry, Medicine
- International journal of molecular sciences
- 2018

A novel multi-epitope peptide, containing Cit-Gly and Ala-Cit motifs in two–two copies, separated with a short, neutral spacer, suitable to develop better diagnostics and novel therapies for RA. Expand