Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments

By Keith A. Baggerly, Jeffrey S. Morris, Kevin R. Coombes. Bioinform., 2004

638 citations recorded by the source corpus.

Subfields: Spectroscopy, Structural Biology

View Paper: https://www.semanticscholar.org/paper/0a7659bb872009ed951dad545b47dc91e7109adc

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Citations in the corpus

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology (2009, neutral): “One theme that emerges is that the most common errors are simple (e.g., row or column offsets); conversely, it is our experience that the most simple errors are common.”
Statistical Analyses and Reproducible Research (2007, background): “Baggerly, Morris, and Coombes (2004) demonstrated many of the problems that can arise when using standard publication formats together with author supplied data.”
Statistical strategies for avoiding false discoveries in metabolomics and related experiments (2007, background): “The fact that this was probably true of the famous ovarian cancer proteomics data soon led to the discovery (Baggerly et al., 2004; Diamandis, 2004) that the original data (Petricoin et al.”
Revisiting biomarker discovery by plasma proteomics (2017, background): “Claims of early cancer detection based on very low-resolution MALDI spectra of plasma that produced patterns but no protein identifications (Petricoin et al, 2002) have not been substantiated (Baggerly et al, 2004), and these technologies have largely been abandoned today.”
Proposed minimum reporting standards for data analysis in metabolomics (2007, background): “This is the easiest way to allow the community swiftly to validate such claims (or otherwise), and was instrumental in the rapid unmasking of artefacts in some well-publicized proteomic biomarker experiments (Baggerly et al., 2004).”
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum (2005, methodology): “It has been shown that the use of inadequate or ineffective methods in the first step may make it difficult to extract meaningful biological information from these data (Sorace and Zhan, 2003; Baggerly et al., 2003, 2004).”