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Functional normalization of 450k methylation array data improves replication in large cancer studies

Overview of attention for article published in Genome Biology (Online Edition), December 2014
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (93rd percentile)
  • Good Attention Score compared to outputs of the same age and source (65th percentile)

Mentioned by

twitter
35 tweeters
facebook
2 Facebook pages

Citations

dimensions_citation
343 Dimensions

Readers on

mendeley
315 Mendeley
citeulike
3 CiteULike
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Title
Functional normalization of 450k methylation array data improves replication in large cancer studies
Published in
Genome Biology (Online Edition), December 2014
DOI 10.1186/s13059-014-0503-2
Pubmed ID
Authors

Jean-Philippe Fortin, Aurélie Labbe, Mathieu Lemire, Brent W Zanke, Thomas J Hudson, Elana J Fertig, Celia MT Greenwood, Kasper D Hansen

Abstract

We propose an extension to quantile normalization that removes unwanted technical variation using control probes. We adapt our algorithm, functional normalization, to the Illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. Using data sets from The Cancer Genome Atlas and a large case-control study, we show that our algorithm outperforms all existing normalization methods with respect to replication of results between experiments, and yields robust results even in the presence of batch effects. Functional normalization can be applied to any microarray platform, provided suitable control probes are available.

Twitter Demographics

The data shown below were collected from the profiles of 35 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 315 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 2%
United Kingdom 3 <1%
Spain 2 <1%
Canada 1 <1%
Sweden 1 <1%
Switzerland 1 <1%
Unknown 302 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 93 30%
Researcher 70 22%
Student > Master 34 11%
Student > Bachelor 26 8%
Student > Doctoral Student 23 7%
Other 42 13%
Unknown 27 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 97 31%
Biochemistry, Genetics and Molecular Biology 93 30%
Medicine and Dentistry 23 7%
Computer Science 21 7%
Neuroscience 11 3%
Other 22 7%
Unknown 48 15%

Attention Score in Context

This research output has an Altmetric Attention Score of 22. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 January 2016.
All research outputs
#978,166
of 16,126,516 outputs
Outputs from Genome Biology (Online Edition)
#966
of 3,434 outputs
Outputs of similar age
#19,485
of 309,383 outputs
Outputs of similar age from Genome Biology (Online Edition)
#30
of 88 outputs
Altmetric has tracked 16,126,516 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,434 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 25.9. This one has gotten more attention than average, scoring higher than 71% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 309,383 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 93% of its contemporaries.
We're also able to compare this research output to 88 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.