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The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
2006
Nature Biotechnology
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and the MAQC web site (http://www.fda.gov/nctr/science/centers/ toxicoinformatics/maqc/). ...
All data are available through GEO (series accession number: GSE5350), ArrayExpress (accession number: E-TABM-132), ArrayTrack (http://www.fda.gov/nctr/science/centers/toxicoinformatics/Array Track/), ...
The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. ...
doi:10.1038/nbt1239
pmid:16964229
pmcid:PMC3272078
fatcat:artpc4ivune53euk2xcfbcocui
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
2010
Nature Biotechnology
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In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity ...
Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. ...
There the MicroArray Quality control (MAQc)-ii study of common practices for the development and validation of microarray-based predictive models As part of the United States Food and Drug Administration's ...
doi:10.1038/nbt.1665
pmid:20676074
pmcid:PMC3315840
fatcat:7ff44lokvrehraq6gdulu3t34q
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study
2008
BMC Genomics
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The MicroArray Quality Control (MAQC) project evaluated the inter-and intra- ...
Approval does not signify that the contents necessarily reflect the position or opinions of the FDA nor does mention of trade names or commercial products constitute endorsement or recommendation for use ...
Acknowledgements This document has been reviewed in accordance with United States Food and Drug Administration (FDA) policy and approved for publication. ...
doi:10.1186/1471-2164-9-328
pmid:18620571
pmcid:PMC2491643
fatcat:visep753eves7mp3xnspsm4n6m
Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project
2006
Nature Biotechnology
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Here we provide a simultaneous comparison of results from one-and two-color labeling designs, using two independent RNA samples from the MicroArray Quality Control (MAQC) project, tested on each of three ...
, data analysis and data interpretation. ...
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project when planning a microarray experiment is whether to use a one-color or two-color approach ...
doi:10.1038/nbt1242
pmid:16964228
fatcat:flc6h5nienao3h7ceagi3vmh64
Power and limitations of RNA-Seq: findings from the SEQC (MAQC-III) Consortium
2015
EMBnet journal
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We present primary results from the Sequencing Quality Control (SEQC) project by US-FDA MAQC consortium. ...
Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. ...
We present primary results from the Sequencing Quality Control (SEQC) project by US-FDA MAQC consortium. ...
doi:10.14806/ej.21.a.831
fatcat:mux5zxplsvdqtdqvtvzoln5tza
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples
2010
BMC Bioinformatics
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Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005. ...
The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. ...
ZW was supported by a postdoctoral fellowship from the National Center for Toxicological Research of the US FDA through the Oak Ridge Institute for Science and Education (ORISE). ...
doi:10.1186/1471-2105-11-s6-s10
pmid:20946593
pmcid:PMC3026357
fatcat:utrpufn6dndcnhy2dx5okymz3u
Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
2007
BMC Bioinformatics
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Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms. ...
The MAQC analysis presented for the conclusion of inter-and intra-platform comparability/ reproducibility of microarray gene expression measurements is inadequate. ...
Acknowledgements The views presented in this paper are those of the authors and do not necessarily represent those of the U.S. Food and Drug Administration. ...
doi:10.1186/1471-2105-8-412
pmid:17961233
pmcid:PMC2204045
fatcat:vw7sxeacjvannjfk3ocvftpxoa
Feature Selection and Classification of MAQC-II Breast Cancer and Multiple Myeloma Microarray Gene Expression Data
2009
PLoS ONE
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Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. ...
Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are ...
The MAQC-II consortium for making the data sets available to this study is gratefully appreciated.
Author Contributions Conceived and designed the experiments: QL. Performed the experiments: QL. ...
doi:10.1371/journal.pone.0008250
pmid:20011240
pmcid:PMC2789385
fatcat:wgvmaxq335cnfjcnggqivdiooi
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
2010
Preserved Fulltext
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In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity ...
Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. ...
All MAQC-II participants freely donated their time and reagents for the completion and analyses of the MAQC-II project. The MAQC-II consortium also thanks R. ...
doi:10.17615/5bpt-a893
fatcat:ptgq4bk3dvdszhlk64ihw4ixyy
Data quality in genomics and microarrays
2006
Nature Biotechnology
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Analysis of the MAQC and ERCC RNA sets has resulted in extensive gene expression data sets with validation across many microarray platforms and systems (e.g., by ...
To date, the MicroArray Quality Control (MAQC) project-the first results of which are presented in this issue-and the External RNA Controls Consortium (ERCC) are the most comprehensive efforts in assessing ...
A vital part of the MAQC project has been the identification of common transcripts that are mutually represented among the various microarray platforms included in the analysis 9 . ...
doi:10.1038/nbt0906-1112
pmid:16964224
pmcid:PMC2943412
fatcat:35hkslbwobf5pck434jftodygq
The FDA's Experience with Emerging Genomics Technologies—Past, Present, and Future
2016
AAPS Journal
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The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing. ...
MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation. ...
The SEQC project evaluated technical performance, quality control, and cross lab and cross platform reproducibility of RNA-seq. ...
doi:10.1208/s12248-016-9917-y
pmid:27116022
pmcid:PMC4973466
fatcat:anbltnjsvranpeedu3quqwhm2u
Shambhala: a platform-agnostic data harmonizer for gene expression data
2019
BMC Bioinformatics
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Each profile is transformed to make it similar to the output of microarray hybridization platform Affymetrix Human Gene. ...
Results: Unlike previously published methods enabling good quality data harmonization for only two datasets, Shambhala allows conversion of multiple datasets into the universal form suitable for further ...
All the gene expression data that were used for research, including the datasets from MAQC, SEQC and GTEx projects, were taken from publicly available repository Gene Expression Omnibus (GEO), and had ...
doi:10.1186/s12859-019-2641-8
fatcat:eldsaomt3vcylestzlm7wfvoia
Of genomics and bioinformatics
2010
The Pharmacogenomics Journal
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The first phase of the MAQC project (MAQC-I) evaluated various issues related to microarray technology, including, but not limited to, quality control, data analysis, cross-laboratory and cross-platform ...
An important parallel research effort is the MicroArray Quality Control (MAQC) project. ...
doi:10.1038/tpj.2010.59
pmid:20676063
fatcat:sydljwli35aapeavn42jwxa6k4
Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)
2009
BMC Proceedings
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We also thank Rosetta Biosoftware and JMP Genomics for sponsoring the conference and all the MAQC special session presenters, poster presenters and student presenters for participating in the conference ...
Acknowledgements We thank Juliebeth Briseno for her assistance with organizing TIES-2007, Chris Smith for the development and maintenance of the conference web site, Rita Ross for help with on-site registration ...
In addition, a special session on the FDA-led MicroArray Quality Control project [2, 3] was provided that highlighted reproducibil-ity of microarray analysis. ...
doi:10.1186/1753-6561-3-s2-s1
pmid:19278557
pmcid:PMC2654484
fatcat:h46bevxh2rg6zkrigwubnmryrq
Arrays of Hope
2006
Cell
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"That allows us to maximally control the quality of the results," says Bernards, avoiding problems that arise from different methods of sample han dling and analysis. ...
"The compa nies controlled the use of their own platforms so the MAQC project had the best of the best working on it," says Kim. "Most labs can do one platform or at the most two very well. ...
doi:10.1016/j.cell.2006.11.005
pmid:17110319
fatcat:nfdfqhnrz5e77piv32l6cdfab4
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