RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.

Autor:	Shehwana H; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Kumar SV; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Melott JM; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Rohrdanz MA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Wakefield C; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Ju Z; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Siwak DR; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Lu Y; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Broom BM; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Weinstein JN; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Mills GB; Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science Center, Portland, OR 97210, USA., Akbani R; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2022 Nov 15; Vol. 38 (22), pp. 5131-5133.
DOI:	10.1093/bioinformatics/btac665
Abstrakt:	Summary: Reverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170 000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, 'noise', that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting. Availability and Implementation: The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE). Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2022. Published by Oxford University Press.)
Databáze:	MEDLINE
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